A structural analysis of the nsp9 protein from the coronavirus MERS CoV reveals a conserved RNA binding interface.

Middle East respiratory syndrome coronavirus (MERS CoV) and severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) are RNA viruses from the Betacoronavirus family that cause serious respiratory illness in humans. One of the conserved non-structural proteins encoded for by the coronavirus family is non-structural protein 9 (nsp9). Nsp9 plays an important role in the RNA capping process of the viral genome, where it is covalently linked to viral RNA (known as RNAylation) by the conserved viral polymerase, nsp12. Nsp9 also directly binds to RNA; we have recently revealed a distinct RNA recognition interface in the SARS CoV-2 nsp9 by using a combination of nuclear magnetic resonance spectroscopy and biolayer interferometry. In this study, we have utilized a similar methodology to determine a structural model of RNA binding of the related MERS CoV. Based on these data, we uncover important similarities and differences to SARS CoV-2 nsp9 and other coronavirus nsp9 proteins. Our findings that replacing key RNA binding residues in MERS CoV nsp9 affects RNAylation efficiency indicate that recognition of RNA may play a role in the capping process of the virus.

A Biochemical and Biophysical Analysis of the Interaction of nsp9 with nsp12 from SARS-CoV-2-Implications for Future Drug Discovery Efforts.

The ongoing global pandemic of the coronavirus 2019 (COVID-19) disease is caused by the virus SARS-CoV-2, with very few highly effective antiviral treatments currently available. The machinery responsible for the replication and transcription of viral RNA during infection is made up of several important proteins. Two of these are nsp12, the catalytic subunit of the viral polymerase, and nsp9, a cofactor of nsp12 involved in the capping and priming of viral RNA. While several recent studies have determined the structural details of the interaction of nsp9 with nsp12 in the context of RNA capping, very few biochemical or biophysical details are currently available. In this study, we have used a combination of surface plasmon resonance (SPR) experiments, size exclusion chromatography (SEC) experiments, and biochemical assays to identify specific nsp9 residues that are critical for nsp12 binding as well as RNAylation, both of which are essential for the RNA capping process. Our data indicate that nsp9 dimerization is unlikely to play a significant functional role in the virus. We confirm that a set of recently discovered antiviral peptides inhibit nsp9-nsp12 interaction by specifically binding to nsp9; however, we find that these peptides do not impact RNAylation. In summary, our results have important implications for future drug discovery efforts to combat SARS-CoV-2 and any newly emerging coronaviruses.

MIBG avidity correlates with clinical features, tumor biology, and outcomes in neuroblastoma: A report from the Children's Oncology Group.

BACKGROUND: Prior studies suggest that neuroblastomas that do not accumulate metaiodobenzylguanidine (MIBG) on diagnostic imaging (MIBG non-avid) may have more favorable features compared with MIBG avid tumors. We compared clinical features, biologic features, and clinical outcomes between patients with MIBG nonavid and MIBG avid neuroblastoma. PROCEDURE: Patients had metastatic high- or intermediate-risk neuroblastoma and were treated on Children's Oncology Group protocols A3973 or A3961. Comparisons of clinical and biologic features according to MIBG avidity were made with chi-squared or Fisher exact tests. Event-free (EFS) and overall (OS) survival compared using log-rank tests and modeled using Cox models. RESULTS: Thirty of 343 patients (8.7%) had MIBG nonavid disease. Patients with nonavid tumors were less likely to have adrenal primary tumors (34.5 vs. 57.2%; P = 0.019), bone metastases (36.7 vs. 61.7%; P = 0.008), or positive urine catecholamines (66.7 vs. 91.0%; P < 0.001) compared with patients with MIBG avid tumors. Nonavid tumors were more likely to be MYCN amplified (53.8 vs. 32.6%; P = 0.030) and had lower norepinephrine transporter expression. Patients with MIBG nonavid disease had a 5-year EFS of 50.0% compared with 38.7% for patients with MIBG avid disease (P = 0.028). On multivariate testing in high-risk patients, MIBG avidity was the sole adverse prognostic factor for EFS identified (hazard ratio 1.77; 95% confidence interval 1.04-2.99; P = 0.034). CONCLUSIONS: Patients with MIBG nonavid neuroblastoma have lower rates of adrenal primary tumors, bone metastasis, and catecholamine secretion. Despite being more likely to have MYCN-amplified tumors, these patients have superior outcomes compared with patients with MIBG avid disease.

Medulloblastoma Down Under 2013: a report from the third annual meeting of the International Medulloblastoma Working Group.

Medulloblastoma is curable in approximately 70% of patients. Over the past decade, progress in improving survival using conventional therapies has stalled, resulting in reduced quality of life due to treatment-related side effects, which are a major concern in survivors. The vast amount of genomic and molecular data generated over the last 5-10 years encourages optimism that improved risk stratification and new molecular targets will improve outcomes. It is now clear that medulloblastoma is not a single-disease entity, but instead consists of at least four distinct molecular subgroups: WNT/Wingless, Sonic Hedgehog, Group 3, and Group 4. The Medulloblastoma Down Under 2013 meeting, which convened at Bunker Bay, Australia, brought together 50 leading clinicians and scientists. The 2-day agenda included focused sessions on pathology and molecular stratification, genomics and mouse models, high-throughput drug screening, and clinical trial design. The meeting established a global action plan to translate novel biologic insights and drug targeting into treatment regimens to improve outcomes. A consensus was reached in several key areas, with the most important being that a novel classification scheme for medulloblastoma based on the four molecular subgroups, as well as histopathologic features, should be presented for consideration in the upcoming fifth edition of the World Health Organization's classification of tumours of the central nervous system. Three other notable areas of agreement were as follows: (1) to establish a central repository of annotated mouse models that are readily accessible and freely available to the international research community; (2) to institute common eligibility criteria between the Children's Oncology Group and the International Society of Paediatric Oncology Europe and initiate joint or parallel clinical trials; (3) to share preliminary high-throughput screening data across discovery labs to hasten the development of novel therapeutics. Medulloblastoma Down Under 2013 was an effective forum for meaningful discussion, which resulted in enhancing international collaborative clinical and translational research of this rare disease. This template could be applied to other fields to devise global action plans addressing all aspects of a disease, from improved disease classification, treatment stratification, and drug targeting to superior treatment regimens to be assessed in cooperative international clinical trials.

Outcome after reduced chemotherapy for intermediate-risk neuroblastoma.

BACKGROUND: The survival rate among patients with intermediate-risk neuroblastoma who receive dose-intensive chemotherapy is excellent, but the survival rate among patients who receive reduced doses of chemotherapy for shorter periods of time is not known. METHODS: We conducted a prospective, phase 3, nonrandomized trial to determine whether a 3-year estimated overall survival of more than 90% could be maintained with reductions in the duration of therapy and drug doses, using a tumor biology-based therapy assignment. Eligible patients had newly diagnosed, intermediate-risk neuroblastoma without MYCN amplification; these patients included infants (<365 days of age) who had stage 3 or 4 disease, children (≥365 days of age) who had stage 3 tumors with favorable histopathological features, and infants who had stage 4S disease with a diploid DNA index or unfavorable histopathological features. Patients who had disease with favorable histopathological features and hyperdiploidy were assigned to four cycles of chemotherapy, and those with an incomplete response or either unfavorable feature were assigned to eight cycles. RESULTS: Between 1997 and 2005, a total of 479 eligible patients were enrolled in this trial (270 patients with stage 3 disease, 178 with stage 4 disease, and 31 with stage 4S disease). A total of 323 patients had tumors with favorable biologic features, and 141 had tumors with unfavorable biologic features. Ploidy, but not histopathological features, was significantly predictive of the outcome. Severe adverse events without disease progression occurred in 10 patients (2.1%), including secondary leukemia (in 3 patients), death from infection (in 3 patients), and death at surgery (in 4 patients). The 3-year estimate (±SE) of overall survival for the entire group was 96±1%, with an overall survival rate of 98±1% among patients who had tumors with favorable biologic features and 93±2% among patients who had tumors with unfavorable biologic features. CONCLUSIONS: A very high rate of survival among patients with intermediate-risk neuroblastoma was achieved with a biologically based treatment assignment involving a substantially reduced duration of chemotherapy and reduced doses of chemotherapeutic agents as compared with the regimens used in earlier trials. These data provide support for further reduction in chemotherapy with more refined risk stratification. (Funded by the National Cancer Institute; ClinicalTrials.gov number, NCT00003093.)

Non-insulinoma pancreatogenous hypoglycemia syndrome due to nesidioblastosis following bariatric Roux-en-Y gastric bypass.

A 56-year-old woman with past medical history significant for bariatric Roux-en-Y gastric bypass 3 years prior presented for evaluation of an 8-month history of severe hypoglycemia relieved by intake of carbohydrates associated with syncopal episodes. Inpatient workup revealed endogenous hyperinsulinemia concerning for insulinoma vs. nesidioblastosis. She successfully underwent pancreaticoduodenectomy (Whipple procedure), and pathology report confirmed scattered low-grade intraepithelial neoplasia within the pancreatic parenchyma consistent with nesidioblastosis. The patient has had satisfactory control of glucose levels 30 days out from surgery.

Do bib clips pose a cross-contamination risk at the dental clinic?

Although multiple-use dental napkin holders have a relatively low risk of transmitting infection, they do require disinfection between patients. This study sought to: 1) determine the presence of bacterial load on two types of clips of reusable bib chains after dental procedures at the Endodontics and Orthodontics clinics at Tufts University School of Dental Medicine; and 2) evaluate the effectiveness of disinfecting the clips. These specialty clinics represent a wide spectrum of patients, procedures, and appointment times. Bacterial load on the bib clips was determined immediately following dental treatments-both before and after their disinfection-during morning and afternoon sessions. The results revealed that, after treatments, there was a statistically significant difference when comparing the two clinics for bacterial burden on the clips. Furthermore, there was a statistically significant difference in bacterial load on the two types of clips. Disinfection of the bib clips was highly effective in both clinics. Clinically, the results suggest that due to the nature of the treatment, the demographic population, and the type of bib clips used, patients in different clinics may be exposed to varying bacterial concentrations on the bib clips, and thus to different possible cross-contamination risks. Future analyses will be performed to identify the bacterial species in samples from both pre- and post-disinfected clips, and to determine if they harbor disease-causing bacterial species that can pose a potential, yet undetermined risk for cross-contamination.

Surgical Treatment of Propriospinal Myoclonus: A Case Report.

Propriospinal myoclonus (PSM) is a rare segmental movement disorder characterized by repetitive irregular myoclonic jerks of the trunk and/or axial limbs at the resting state. It is imperative to make a correct diagnosis as other movement disorders can be mistaken for or mask PSM. Therefore, a battery of neuroimaging and neurophysiological testing must be undertaken. In our case report, we discuss a patient who was diagnosed with PSM concurrently with cervical degenerative stenosis and then had a successful outcome via surgical decompression and arthrodesis of the cervical spine. We documented the patient's postoperative course and achievement of complete remission, sustained at a 41-month follow-up. We then grouped our case together with five other PSM cases in the literature to offer readers a broader context of the role of surgical spinal intervention in ameliorating PSM.

Rapidly Progressive Bilateral Vitreoretinal Lymphoma.

A 56-year-old male who presented with unilateral localized sub-retinal lesions suspicious for primary vitreoretinal lymphoma (PVRL) developed florid bilateral ocular involvement and was found to have lesions on MRI of the brain in a five-week period despite the absence of vitreous involvement during the entire course of his disease. His ocular lesions were monitored while on systemic treatment and an excellent clinical response was achieved. His central nervous system (CNS) lesions, however, continued to progress despite chemotherapy and whole-brain radiation. He died 12 months from his time of ocular diagnosis. To our knowledge, this case represents the most rapid progression of PVRL reported in the literature - from unilateral, localized lesions in the sub-retinal space to bilateral ocular involvement and identification of CNS involvement in a five-week period. This case highlights the potential for rapid ocular progression of PVRL stressing the need for early diagnosis. Therefore, we recommend prompt vitreous and, if necessary, sub-retinal biopsy in cases of suspected vitreoretinal lymphoma in addition to neuro-imaging. We emphasize the importance of coordination between pathologists, ophthalmologists, and oncologists for prompt, accurate diagnosis. Delay in diagnosis and treatment can result in rapid intraocular progression and central nervous system spread.

Gene-based outcome prediction in multiple cohorts of pediatric T-cell acute lymphoblastic leukemia: a Children's Oncology Group study.

BACKGROUND: Continuous complete clinical remission in T-cell acute lymphoblastic leukemia (T-ALL) is now approaching 80% due to the implementation of aggressive chemotherapy protocols but patients that relapse continue to have a poor prognosis. Such patients could benefit from augmented therapy if their clinical outcome could be more accurately predicted at the time of diagnosis. Gene expression profiling offers the potential to identify additional prognostic markers but has had limited success in generating robust signatures that predict outcome across multiple patient cohorts. This study aimed to identify robust gene classifiers that could be used for the accurate prediction of relapse in independent cohorts and across different experimental platforms. RESULTS: Using HG-U133Plus2 microarrays we modeled a five-gene classifier (5-GC) that accurately predicted clinical outcome in a cohort of 50 T-ALL patients. The 5-GC was further tested against three independent cohorts of T-ALL patients, using either qRT-PCR or microarray gene expression, and could predict patients with significantly adverse clinical outcome in each. The 5-GC featured the interleukin-7 receptor (IL-7R), low-expression of which was independently predictive of relapse in T-ALL patients. In T-ALL cell lines, low IL-7R expression was correlated with diminished growth response to IL-7 and enhanced glucocorticoid resistance. Analysis of biological pathways identified the NF-kappaB and Wnt pathways, and the cell adhesion receptor family (particularly integrins) as being predictive of relapse. Outcome modeling using genes from these pathways identified patients with significantly worse relapse-free survival in each T-ALL cohort. CONCLUSIONS: We have used two different approaches to identify, for the first time, robust gene signatures that can successfully discriminate relapse and CCR patients at the time of diagnosis across multiple patient cohorts and platforms. Such genes and pathways represent markers for improved patient risk stratification and potential targets for novel T-ALL therapies.

Classic and desmoplastic medulloblastoma: complete case reports and characterizations of two new cell lines.

Medulloblastoma (MB) is the most common type of brain tumor affecting children. These tumors are a significant cause of childhood mortality and morbidity, and more effective and less invasive treatment options are urgently required. To achieve these aims, it will be critical to develop a more comprehensive understanding of the molecular pathogenesis of MB. At present, there are relatively few well-characterized MB cell lines available to the research community for the study of MB molecular and cellular biology. Here we present the case reports of two children diagnosed with classic and desmoplastic MB, and describe the characteristics of two new MB cell lines derived from these individuals. A number of genes encoding components of the sonic hedgehog (SHH) and WNT pathways were up-regulated in the desmoplastic relative to the classic MB cell line consistent with aberrant activation of these pathways in desmoplastic MB. These cell lines represent an additional resource for the analysis of diverse aspects of MB biology.

Prediction of relapse in paediatric pre-B acute lymphoblastic leukaemia using a three-gene risk index.

Despite high cure rates 25% of children with acute lymphoblastic leukaemia (ALL) relapse and have dismal outcome. Crucially, many are currently stratified as standard risk (SR) and additional markers to improve patient stratification are required. Here we have used diagnostic bone marrow specimens from 101 children with pre-B ALL to examine the use of gene expression profiles (GEP) as predictors of long-term clinical outcome. Patients were divided into two cohorts for model development and validation based on availability of specimen material. Initially, GEP from 55 patients with sufficient material were analysed using HG-U133A microarrays, identifying an 18-gene classifier (GC) that was more predictive of outcome than conventional prognostic parameters. After feature selection and validation of expression levels by quantitative reverse transcription polymerase chain reaction (qRT-PCR), a three-gene qRT-PCR risk index [glutamine synthetase (GLUL), ornithine decarboxylase antizyme inhibitor (AZIN), immunoglobulin J chain (IGJ)] was developed that predicted outcome with an accuracy of 89% in the array cohort and 87% in the independent validation cohort. The data demonstrate the feasibility of using GEP to improve risk stratification in childhood ALL. This is particularly important for the identification of patients destined to relapse despite their current stratification as SR, as more intensive front-line treatment options for these individuals are already available.

Detection of hemizygous deletions in genomic DNA from leukaemia specimens for the diagnosis of patients.

Hemizygous deletions in genomic DNA appear to play an important role in tumorigenesis. The loss or inactivation of tumour suppressor genes (TSGs) is of critical importance in most malignancies, and has been shown to affect response to therapy. Here, we report a quantitative real-time polymerase chain reaction (qPCR) designed to detect two TSGs at the CDKN2A locus, p16(INK4A) and p14(ARF) that allows the detection of hemizygous deletions. Testing by qPCR of 18 bone marrow specimens from paediatric acute lymphoblastic leukaemia (ALL) patients at diagnosis revealed nine to be GG, six to be GD and three to be DD for exon 2 of p14(ARF)/p16(INK4A), concordant with Southern blotting analysis. A panel of 13 ALL cell lines was investigated for deletions at the CDKN2A locus and one of the lines, typed as GD for all exons, was further assessed by fluorescence in situ hybridisation, confirming the qPCR findings. The expression levels of p16(INK4A) and p14(ARF) were measured in all cell lines and these quantitative reverse transcriptase PCR results also agreed with the typing by qPCR. The qPCR method described is suitable for detection of hemizygous loss in primary patient material and the accuracy of the method was verified by three independent techniques.

Customization of a standard practice management software program to satisfy the needs of a dental hygiene program.

The University of New England (UNE) Dental Hygiene Program converted from a paper format to a digital format to manage the daily, dental hygiene clinic transactions. The use of this practice management software created new opportunities to enhance the program's teaching mission, monitor the progress of individual students, and facilitate the data collection necessary to meet accreditation standards. This report will describe how this dental hygiene program customized a standard practice management software program to enhance the specific requirements of a clinical teaching institution.

Identification of novel molecular prognostic markers for paediatric T-cell acute lymphoblastic leukaemia.

In the last four decades the survival of patients with newly diagnosed childhood T-cell acute lymphoblastic leukaemia (T-ALL) has improved dramatically. In sharp contrast, relapsed T-ALL continues to confer a dismal prognosis. We sought to determine if gene expression profiling could uncover a signature of outcome for children with T-ALL. Using 12 patient specimens obtained before therapy started, we examined the gene expression profile by oligonucleotide microarrays. We identified three genes, CFLAR, NOTCH2 and BTG3, whose expression at the time of diagnosis accurately distinguished the patients according to disease outcome. These genes are involved in the regulation of apoptosis and cellular proliferation. The prognostic value of the three predictive genes was assessed in an independent cohort of 25 paediatric T-ALL patients using quantitative real-time reverse transcription polymerase chain reaction. Patients assigned to the adverse outcome group had a significantly higher cumulative incidence of relapse compared with patients assigned to the favourable outcome group (46% vs. 8%, P = 0.029). Five-year overall survival was also significantly worse in the patients assigned to the adverse outcome group (P = 0.0039). The independent influence of the 3-gene predictor was confirmed by multivariate analysis. Our study provides proof of principle that genome-wide expression profiling can detect novel molecular prognostic markers in paediatric T-ALL.

Relapse in children with acute lymphoblastic leukemia involving selection of a preexisting drug-resistant subclone.

Relapse following remission induction chemotherapy remains a barrier to survival in approximately 20% of children suffering from acute lymphoblastic leukemia (ALL). To investigate the mechanism of relapse, 27 matched diagnosis and relapse ALL samples were analyzed for clonal populations using polymerase chain reaction (PCR)-based detection of multiple antigen receptor gene rearrangements. These clonal markers revealed the emergence of apparently new populations at relapse in 13 patients. More sensitive clone-specific PCR revealed that, in 8 cases, these "relapse clones" were present at diagnosis and a significant relationship existed between presence of the relapse clone at diagnosis and time to first relapse (P < .007). Furthermore, in cases where the relapse clone could be quantified, time to first relapse was dependent on the amount of the relapse clone at diagnosis (r = -0.84; P = .018). This observation, together with demonstrated differential chemosensitivity between subclones at diagnosis, argues against therapy-induced acquired resistance as the mechanism of relapse in the informative patients. Instead these data indicate that relapse in ALL patients may commonly involve selection of a minor intrinsically resistant subclone that is undetectable by routine PCR-based methods. Relapse prediction may be improved with strategies to detect minor potentially resistant subclones early during treatment, hence allowing intensification of therapy.

Fibrin clot adhesion to dentin conditioned with protein constructs: an in vitro proof-of-principle study.

OBJECTIVES: Periodontal regeneration is contingent on the adsorption, uninterrupted adhesion, and maturation of a fibrin clot to a periodontally compromised root surface. Clot adhesion appears vitally dependent on the formation of a resilient union between the clot and the root surface. Root surface demineralization will remove a root surface smear layer exposing dentin tubules and collagen matrix for enhanced clot adhesion. Recently, protein constructs have been introduced to condition the root during periodontal surgery. The effect of such root conditioning on clot adhesion has not been clarified. The objective of this study was to evaluate clot adhesion to protein conditioned dentin surfaces. METHODS: Human dentin blocks (4 x 6 x 1 mm) were exposed to a saturated citric acid solution (CA) or a commercial ethylenediaminetetraacetic acid (EDTA) preparation using standardized protocols. Some dentin blocks were additionally conditioned with proteins, either bovine serum albumin (BSA) or an enamel matrix protein preparation (EMP). Fresh human whole blood was applied to the blocks. The blood was allowed to clot for 20 min. in a humidified chamber. The dentin blocks were rinsed 3 x 5 min. in phosphate-buffered saline under standardized conditions to test clot adhesion. They were then processed for scanning electron microscopy (SEM). Two masked examiners independently evaluated the SEM images. RESULTS: CA removed the dentin smear layer, exposing dentin tubules and collagen. EDTA appeared less efficacious leaving smear layer residues. The BSA or EMP application resulted in a surface morphology similar to that of a smear layer. Fibrin clot adhesion was best supported by the CA-treated dentin surface. Forces produced by the rinse protocol partially removed the fibrin clot from EDTA-treated surfaces. BSA- or EMP-treated surfaces poorly retained the fibrin clot. CONCLUSIONS: CA surface demineralization removes a dentin surface smear layer to promote adhesion of a fibrin clot. The EDTA gel appears less effective. Further conditioning of the dentin surface with protein constructs produces a surface morphology similar to that of the smear layer with poor fibrin clot retention.

Successful induction and maintenance of long-term remission in a child with chronic relapsing autoimmune hemolytic anemia using rituximab.

Childhood autoimmune hemolytic anemia (AIHA) of the warm type is usually successfully managed with corticosteroids and/or immunoglobulin infusions. In a small proportion of patients AIHA follows a more severe and protracted pathway resulting in the use of immunosuppressive therapy and frequently culminating with the need for splenectomy. Rituximab is an anti-CD20 (B-cell) monoclonal antibody used for the treatment of patients with relapsed or refractory low-grade or follicular, CD20 positive, B-cell non-Hodgkin's lymphoma. Case reports on the use of rituximab for childhood AIHA are scant. The authors describe the first report in which rituximab was effectively employed to induce a long-term remission in a young child with the longest history of chronic relapsing AIHA prior to receiving rituximab. All immunosuppressive therapy was successfully discontinued and splenectomy was avoided.

Utilization of research methodology in designing and developing an interdisciplinary course in ethics.

Development research methodology was utilized to design an interdisciplinary ethics course for students from seven disciplines: dental hygiene, nursing, nurse anesthesia, occupational therapy, physician assistant, physical therapy, and social work. Two research questions, 'What content areas should be considered for inclusion in an interdisciplinary course in Ethics?' and 'What design framework, format, or structure would best fit the content chosen?' guided the study. An interdisciplinary faculty design team conducted a comparative analysis of each of the seven discipline's codes of ethics to find common topics of interest. Further analysis then grouped these topics into eight categories of professional responsibility. The result was a fifteen-week course with validated content relevant to all disciplines.