Cryo-EM Structure of AAV2 Rep68 bound to integration site AAVS1: Insights into the mechanism of DNA melting

The Rep68 protein from Adeno-Associated Virus (AAV) is a multifunctional SF3 helicase that performs most of the DNA transactions required for the viral life cycle. During AAV DNA replication, Rep68 assembles at the origin and catalyzes the DNA melting and nicking reactions during the hairpin rolling replication process to complete the second-strand synthesis of the AAV genome. Here, we report the Cryo-EM structures of Rep68 bound to double-stranded DNA (dsDNA) containing the sequence of the AAVS1 integration site in different nucleotide-bound states. In the apo state, Rep68 forms a heptameric complex around DNA, with three Origin Binding Domains (OBDs) bound to the Rep Binding Site (RBS) sequence and three other OBDs forming transient dimers with them. The AAA+ domains form an open ring with no interactions between subunits and with DNA. We hypothesize the heptameric quaternary structure is necessary to load onto dsDNA. In the ATPγS-bound state, a subset of three subunits binds the nucleotide, undergoing a large conformational change, inducing the formation of intersubunit interactions interaction and interaction with three consecutive DNA phosphate groups. Moreover, the induced conformational change positions three phenylalanine residues to come in close contact with the DNA backbone, producing a distortion in the DNA. We propose that the phenylalanine residues can potentially act as a hydrophobic wedge in the DNA melting process.

Pre-treatment delay and out of pocket expenses by notified new tuberculosis patients in an Indian mega city

BACKGROUND

Study was carried out to find out delay from onset of symptoms and out of pocket expenditure (OOPE) until initiation of anti-TB treatment (ATT) by new Tuberculosis (TB) patients registered in public health facilities in Bengaluru.

METHODS

Notified patients (N = 228) selected purposively were interviewed at initiation of ATT regarding number and type of facilities visited and delay in initiating ATT. OOPE was elicited separately for in- and out-patient visits, towards consultation, purchase of medicines, diagnostic tests, transportation, hospitalization and food. Dissaving or money borrowed was ascertained.

RESULTS

Two-thirds of participants were 15-44 years of age and 56% were males, mean annual household income was $4357. About 75% first visited a private health facility; 68% and 87% respectively were diagnosed and started on ATT in public sector after visiting an average of three facilities and after a mean delay of 68 days; the median delay was 44 days. Of mean OOPE of $402, 54% was direct medical expenditure, 5% non-medical direct and 41% indirect. OOPE was higher for Extra-pulmonary TB compared to PTB and when number of health facilities visited before initiating treatment was >3 compared to those who visited ≤3 and when the time interval between onset of symptoms and treatment initiation (total delay) was >28 days compared to when this interval was ≤28 days. About 20% suffered catastrophic expenditure; 34% borrowed money and 37% sold assets.

CONCLUSION

Concerted efforts are needed to reduce delay and OOPE in pre-treatment period and social protection to account for indirect expenditure.

Neuroendocrine tumors and Survival- a meta-analysis

Introduction/Objective

Neuroendocrine tumors (NET) are a rare group of epithelial neoplasm present in gastrointestinal tract (GI) (67.5%), bronchopulmonary tree (25.3-30%) and in 15% cases primary sites cannot be identified. Although endoscopic screening, improvement in pathological techniques and early detection have shown improvement in NET survival rates, the prognosis is very poor. In this study we aimed to evaluate the effect of Gastrointestinal pancreatic NETs (GEP NETs) grade on overall survival.

Methods/Case Report

We searched observational studies describing the overall survival or prognostic factors of primary GEP NETs from May 2011 -May 2021 following PRISMA guidelines. Studies describing the effect of primary grade 3 GEP NETs on overall survival were included. Meta-analysis was performed and pooled hazard ratio and their 95% confidence interval (95%CI) were obtained. The forest plots were created using random effects models and sensitivity analysis was performed to account for the heterogeneity.

Results (if a Case Study enter NA)

Seven studies with 7692 confirmed patients were included. In our meta-analysis grade 3 GEP NET were associated with higher odds of poor survival (pooled HR: 2.73; 95% CI: 1.36–5.47; p = 0.005), with 92% heterogeneity between studies (p < 0.0001). To account for heterogeneity, sensitivity analysis was performed by removing two outlying studies (Fathi et al. and Foubert et al.) on funnel plots. The results after sensitivity analysis did not change and still showed significant association of grade 3 with poor survival (pooled HR: 4.53; 95% CI: 3.54–5.78; p < 0.00001), with no heterogeneity between studies (p = 0.72; I2 = 0%).

Conclusion

Our meta-analysis found that grade 3 GEP NETs is associated with poor survival and additional future studies are needed to identify other risk factors associated with poor survival in GEP NETs to improve the mortality.

Acute liver failure with amiodarone infusion: A case report and systematic review

WHAT IS KNOWN AND OBJECTIVE

Amiodarone, a commonly used class III antiarrhythmic agent notable for a relatively long half-life of up to 6 months and its pronounced adverse effect profile, is used for both acute and chronic management of cardiac arrhythmias. Chronic use of amiodarone has been associated with asymptomatic hepatotoxicity; however, acute toxicity is thought to be uncommon. There are only six reported cases of acute liver failure (ALF) secondary to amiodarone. In all these cases the outcome of death during the same hospitalization resulted. We aimed to report the only case of acute liver failure secondary to amiodarone infusion in the existing literature where the patient survived.

CASE SUMMARY

A 79-year-old woman admitted with atrial flutter was being treated with intravenous (IV) amiodarone when she abruptly developed coagulopathy, altered mental status and liver enzyme derangement. She was diagnosed with acute liver failure (ALF) secondary to an amiodarone adverse drug reaction, with a calculated score of seven on the Naranjo adverse drug reaction probability scale. Amiodarone was immediately withheld, and N-acetylcysteine (NAC) was initiated. Clinical improvement was seen within 48 hours of holding the drug and within 24 hours of initiating NAC. On post-hospital follow-up visit she was reported to have complete recovery.

WHAT IS NEW AND CONCLUSION

This report emphasizes the importance of monitoring liver enzymes and mental status while a patient is being administered IV amiodarone. N-acetylcysteine administration may have possibly contributed to the early and successful recovery from ALF in our patient. To date, she is the only patient in the existing literature who has been reported to survive ALF secondary to amiodarone administration.

HELLP syndrome--a pregnancy disorder with poor prognosis

HELLP syndrome is a pregnancy-specific disorder defined by hemolysis, elevated liver enzymes and low platelet count that is found in parturients, more frequent in older multiparas. It is frequently associated with severe preeclampsia or eclampsia, but can also be diagnosed in the absence of these disorders. The etiology of HELLP syndrome is unknown, and the pathogenesis of this disorder (including the hepatological manifestations) is not fully understood. The most widely accepted hypotheses are: a change in the immune feto-maternal balance, platelet aggregation, endothelial dysfunction, arterial hypertension and an inborn error of the fatty acid oxidative metabolism. Hepatic involvement occurs by intravascular fibrin deposition and hypovolemia. Serum LDH and platelet count are the two most important clinical tools for disease assessment. LDH reflects both the extent of hemolysis and hepatic dysfunction. Maternofetal complications cause a 7.0-70.0% perinatal mortality rate and a 1.0-24.0% maternal mortality rate. The recognition of HELLP syndrome and an aggressive multidisciplinary approach and prompt transfer of these women to obstetric centers with expertise in this field are required for the improvement of materno-fetal prognosis.

Development and evaluation of an In vitro isolation of street rabies virus in mouse neuroblastoma cells as compared to conventional tests used for diagnosis of rabies

In vitro isolation of rabies virus using mouse neuroblastoma cells (MNA) was evaluated. The sensitivity and reliability of in vitro procedure was performed in comparison with mouse inoculation test (MIT), the in vivo method of virus isolation, direct fluorescent antibody test (FAT) and Sellers staining. Of the 33 animal brain samples tested, 24 (72.72%) were positive by MIT. Sensitivity of Sellers stain, FAT and rapid tissue culture infection test (RTCIT) was found to be 54.16, 100 and 91.6% respectively. Concordance of Sellers stain, FAT, RTCIT with MIT was found to be 66.6, 100 and 93.93% respectively. Two samples which were positive by FAT and MIT showed gross contamination in cell lines, which is one of the drawbacks of RTCIT. However, rabies virus could be isolated in MNA cells from two of the eight human cerebrospinal fluid (CSF) samples from clinico-epidemiologically suspected cases of rabies. Both MIT and FAT showed negative results in the two CSF samples. RTCIT appears to be a fast and reliable alternative to MIT and holds promise in antemortem diagnosis of rabies, which is otherwise, a challenging task for a reference laboratory.

Tumor necrosis factor and reactive oxygen species cooperative cytotoxicity is mediated via inhibition of NF-kappaB

BACKGROUND

Tumor necrosis factor alpha (TNFalpha) plays a key role in pathogenesis of brain injury. However, TNFalpha exhibits no cytotoxicity in primary cultures of brain cells. This discrepancy suggests that other pathogenic stimuli that exist in the setting of brain injury precipitate TNFalpha cytotoxicity. The hypothesis was tested that reactive oxygen species (ROS), that are released early after brain injury, act synergistically with TNFalpha in causing cell death.

MATERIALS AND METHODS

Cultured human and rat brain capillary endothelial cells (RBEC), and cortical astrocytes were treated with TNFalpha alone or together with different doses of H2O2, and apoptotic cell death and DNA fragmentation were measured by means of 3'-OH-terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) and Hoechst fluorescence assay, respectively. The effect of H2O2 on TNFalpha-induced activation of nuclear factor kappa B (NF-kappaB) was measured by Western blots of cytoplasmic and nuclear extracts of RBEC using anti-inhibitor of NF-kappaB (IkappaB) and anti-p65 subunit of NF-kappaB antibodies. Nuclear translocation of NF-kappaB was investigated by immunofluorescent staining of RBEC with anti-p65 antibodies.

RESULTS

TNFalpha alone had no cytotoxic effect in brain endothelial cells and astrocytes at concentrations up to 100 ng/ml. Co-treatment with 5-10 microM of H2O2 caused a two-fold increase in the number of apoptotic cells 24 hr later. Similar doses (1-3 microM) of H2O2 initiated early DNA fragmentation. H2O2 inhibited TNFalpha-induced accumulation of p65 in the nucleus, although it had no effect on degradation of the IkappaB in cytoplasm. Immunostaining confirmed that H2O2 inhibited p65 transport to the nucleus.

CONCLUSIONS

Reactive oxygen species could act synergistically with TNFalpha in causing cytotoxicity via inhibition of a cytoprotective branch of TNFalpha signaling pathways, which starts with NF-kappaB activation.

Activation of peroxisome proliferator-activated receptor-gamma pathway inhibits osteoclast differentiation

The nuclear receptor and transcription factor, peroxisome proliferator-activated receptor-gamma (PPAR-gamma), regulates the activity of other transcription factors in the adipogenic differentiation and inflammatory response pathways. We examined the possible function of the PPAR-gamma pathway in osteoclast (Ocl) formation from CD34(+) hematopoietic stem cells (CD34(+) HSCs), using a co-culture system comprised of human mesenchymal stem cells (hMSCs) and CD34(+) HSCs, both derived from bone marrow. Ocl formation in this co-culture system is enhanced by the addition of exogenous osteoprotegerin ligand (OPGL), an essential Ocl differentiation factor, and macrophage-colony stimulating factor (M-CSF). The data indicate that soluble OPGL (sOPGL) and M-CSF stimulate Ocl formation in the co-cultures up to 4-fold compared with CD34(+) HSCs alone treated with sOPGL and M-CSF. CD34(+) HSCs, but not hMSCs, express PPAR-gamma, and 15-deoxy-Delta(12, 14)-prostaglandin-J2 (15d-PG-J2), a PPAR-gamma agonist, completely blocked the effects of sOPGL and M-CSF on Ocl formation and activity. The inhibitory effect of 15d-PG-J2 is specific to the Ocl lineage in both human and mouse models of osteoclastogenesis. Accordingly, parallel experiments demonstrate that sOPGL activates the NF-kappaB pathway within mouse Ocl progenitors, and this effect was abolished by 15d-PG-J2. These data establish a link between PPAR-gamma and OPGL signaling within Ocl progenitors, and support a role for PPAR-gamma pathway in the modulation of osteoclastogenesis.