Fluorescence-resonance-energy-transfer-based assay to estimate modulation of TDP1 activity through arginine methylation

Tyrosyl DNA phosphodiesterase (TDP1) is a DNA repair enzyme that hydrolyzes the phosphotyrosyl linkage between 3'-DNA-protein crosslinks such as stalled topoisomerase 1 cleavage complexes (Top1cc). Here, we present a fluorescence-resonance-energy-transfer-(FRET) based assay to estimate modulation of TDP1 activity through arginine methylation. We describe steps for TDP1 expression and purification and estimating TDP1 activity using fluorescence-quenched probes mimicking Top1cc. We then detail data analysis of real-time TDP1 activity and screening of TDP1-selective inhibitors. For complete details on the use and execution of this protocol, please refer to Bhattacharjee et al. (2022).¹.

Interplay between symmetric arginine dimethylation and ubiquitylation regulates TDP1 proteostasis for the repair of topoisomerase I-DNA adducts

Tyrosyl-DNA phosphodiesterase (TDP1) hydrolyzes the phosphodiester bond between a DNA 3' end and a tyrosyl moiety and is implicated in the repair of trapped topoisomerase I (Top1)-DNA covalent complexes (Top1cc). Protein arginine methyltransferase 5 (PRMT5) catalyzes arginine methylation of TDP1 at the residues R361 and R586. Here, we establish mechanistic crosstalk between TDP1 arginine methylation and ubiquitylation, which is critical for TDP1 homeostasis and cellular responses to Top1 poisons. We show that R586 methylation promotes TDP1 ubiquitylation, which facilitates ubiquitin/proteasome-dependent TDP1 turnover by impeding the binding of UCHL3 (deubiquitylase enzyme) with TDP1. TDP1-R586 also promotes TDP1-XRCC1 binding and XRCC1 foci formation at Top1cc-damage sites. Intriguingly, R361 methylation enhances the 3'-phosphodiesterase activity of TDP1 in real-time fluorescence-based cleavage assays, and this was rationalized using structural modeling. Together, our findings establish arginine methylation as a co-regulator of TDP1 proteostasis and activity, which modulates the repair of trapped Top1cc.

Chronic diarrhea - The poetic masquerade

Chronic diarrhea, by definition, is the passage of loose/liquid stools, with increased frequency (more than three times/day), or an output of over 200 g/day, lasting for a duration of four or more weeks. The clinical approach to identify the cause of chronic diarrhea generally depends on the local socioeconomic status. In high-income countries, systemic causes such as irritable bowel syndrome (IBS), inflammatory bowel disease, malabsorption syndromes (lactose intolerance/coeliac disease) are primarily considered. In mid- to low-income countries, infective causes like chronic bacterial, mycobacterial, fungal infections, HIV, bowel cancer are considered before systemic causes/malabsorption syndromes. Amyloidosis, more accurately, reactive amyloidosis is one of the rarer causes of chronic/persistent diarrhea. Inflammatory colitis secondary to POEMS syndrome (polyneuropathy, organomegaly, endocrinopathy, monoclonal gammopathy, and skin changes) as a cause for chronic diarrhea has been reported only in a handful of cases and is often missed. We present such a case of chronic diarrhea in a middle-aged man, who was eventually diagnosed to have POEMS syndrome.

Pattern of Glomerular Disease in a Tertiary Care Hospital of Bangladesh

Glomerular disease is one of the most important causes of chronic kidney disease in developing countries like Bangladesh as well as the whole world. The pattern of glomerular disease varies in different countries and can have different clinical presentations. The aim of the study was to analyze the clinical profile and to determine the histological pattern of glomerular diseases in a large tertiary care hospital in Bangladesh. All kidney biopsies performed in Mymensingh Medical College Hospital, Bangladesh from October 2018 to March 2020 were prospectively analyzed in the study. A total of 101 patients with kidney biopsy were examined by clinical and laboratory findings and by light and immuno-fluorescence microscopy. The mean age was 30.0±14.6 years and 50(49.5%) were male and 51(50.5%) were female with a male to female ratio of 1:1. The clinical syndromes namely nephrotic syndrome, nephritic syndrome, nephrito-nephrotic presentation, RPGN like presentation, macroscopic haematuria and asymptomatic urine abnormality were present in 31.7%, 34.5%, 22.8%, 11.9%, 19.8% and 10.9% patients respectively. The most common histological varieties found in the study were mesangial proliferative glomerulonephritis (MesPGN) (18.8%) and focal segmental glomerulosclerosis (FSGS) (18.8%). Other histopathological pattern among the studied subjects revealed minimal change disease (MCD) in 5.9%, membranous nephropathy (MN) in 7.9%, membranoproliferative glomerulonephritis (MPGN) in 16.8%, IgA nephropathy in 5%, IgM nephropathy in 2%, IgG nephropathy in 2%, diffuse proliferative glomerulonephritis (DPGN) in 1%, focal proliferative glomerulo-nephritis (FPGN) in 3%, crescentic GN in 3%, lupus nephritis (LN) in 13.9%, amyloidosis in 1% and fibrillary glomerulopathy in 1% patient. The pattern of glomerular disease found in this study was similar to other studies performed in Bangladesh with a little variation. It may guide the future researchers to establish a national kidney biopsy registry in Bangladesh.

0717 Peer-intervention Can Reduce Health Disparities In Patients With Obstructive Sleep Apnea

Introduction

In patients with obstructive sleep apnea (OSA), adherence to continuous positive airway pressure (CPAP) therapy is a major problem. Moreover, up to 20% of patients with suspected OSA who are referred to sleep study testing do not adhere to such diagnostic work-up. Although, peer-driven intervention with an interactive voice response system (PDI-IVR) can improve CPAP adherence, whether such an intervention can improve adherence to sleep study testing is unknown. Also, there remain health disparities with greater levels of CPAP nonadherence disproportionately affecting individuals of lower socioeconomic status. We aimed to determine whether PDI-IVR can improve adherence to sleep study testing and CPAP adherence in a lower income population.

Methods

We performed a prospective, randomized, parallel group, controlled trial wherein patients with suspected OSA were randomly assigned to receive PDI-IVR or provided with educational information regarding OSA and CPAP therapy (attention-control group) while both groups received usual care. The PDI-IVR interactions aimed at promoting adherence to sleep study testing and in patients diagnosed with OSA the peer-intervention was focused on improving CPAP adherence. In the PDI-IVR group, trained peers (peer-buddies) with OSA were paired with randomized patients over a 6-month period combined with an ability to meet in-person, email, text message, or phone an inter-disciplinary team of providers.

Results

In this pilot study, there were 63 patients (48.4 ± 12.5 years; 30 men) who were randomized to intervention (n=31) and attention-control (n=32) arms. There were 36 peer-buddies who mentored the patients in the intervention group. Intention to treat analysis revealed that failure to undergo sleep study testing was 15.6% of patients in the attention-control arm and 9.7% in the PDI-IVR arm (P=0.7). Per protocol analysis revealed that failure to undergo sleep study testing was 18.4% of patients in the attention-control arm and 4% in the PDI-IVR arm (P=0.13). At 6 months, CPAP adherence was greater in PDI-IVR arm (290 ± 45 min [SE]) than attention-control arm (181 ± 43 min; P=0.01).

Conclusion

In a lower income population, PDI-IVR improved CPAP adherence with a tendency for better adherence to sleep-study testing. Peer-intervention can reduce sleep health disparities.

Support

HL138377

SCAN1-TDP1 trapping on mitochondrial DNA promotes mitochondrial dysfunction and mitophagy

A homozygous mutation of human tyrosyl-DNA phosphodiesterase 1 (TDP1) causes the neurodegenerative syndrome, spinocerebellar ataxia with axonal neuropathy (SCAN1). TDP1 hydrolyzes the phosphodiester bond between DNA 3'-end and a tyrosyl moiety within trapped topoisomerase I (Top1)-DNA covalent complexes (Top1cc). TDP1 is critical for mitochondrial DNA (mtDNA) repair; however, the role of mitochondria remains largely unknown for the etiology of SCAN1. We demonstrate that mitochondria in cells expressing SCAN1-TDP1 (TDP1^H493R) are selectively trapped on mtDNA in the regulatory non-coding region and promoter sequences. Trapped TDP1^H493R-mtDNA complexes were markedly increased in the presence of the Top1 poison (mito-SN38) when targeted selectively into mitochondria in nanoparticles. TDP1^H493R-trapping accumulates mtDNA damage and triggers Drp1-mediated mitochondrial fission, which blocks mitobiogenesis. TDP1^H493R prompts PTEN-induced kinase 1-dependent mitophagy to eliminate dysfunctional mitochondria. SCAN1-TDP1 in mitochondria creates a pathological state that allows neurons to turn on mitophagy to rescue fit mitochondria as a mechanism of survival.

PRMT5-mediated arginine methylation of TDP1 for the repair of topoisomerase I covalent complexes

Human tyrosyl-DNA phosphodiesterases (TDP) hydrolyze the phosphodiester bond between DNA and the catalytic tyrosine of Top1 to excise topoisomerase I cleavage complexes (Top1cc) that are trapped by camptothecin (CPT) and by genotoxic DNA alterations. Here we show that the protein arginine methyltransferase PRMT5 enhances the repair of Top1cc by direct binding to TDP1 and arginine dimethylation of TDP1 at residues R361 and R586. Top1-induced replication-mediated DNA damage induces TDP1 arginine methylation, enhancing its 3'- phosphodiesterase activity. TDP1 arginine methylation also increases XRCC1 association with TDP1 in response to CPT, and the recruitment of XRCC1 to Top1cc DNA damage foci. PRMT5 knockdown cells exhibit defective TDP1 activity with marked elevation in replication-coupled CPT-induced DNA damage and lethality. Finally, methylation of R361 and R586 stimulate TDP1 repair function and promote cell survival in response to CPT. Together, our findings provide evidence for the importance of PRMT5 for the post-translational regulation of TDP1 and repair of Top1cc.

Accuracy of quick Sequential Organ Failure Assessment (qSOFA) score and systemic inflammatory response syndrome (SIRS) criteria for predicting mortality in hospitalized patients with suspected infection: a meta-analysis of observational studies

OBJECTIVE

To identify sensitivity, specificity and predictive accuracy of quick sequential organ failure assessment (qSOFA) score and systemic inflammatory response syndrome (SIRS) criteria to predict in-hospital mortality in hospitalized patients with suspected infection.

METHODS

This meta-analysis followed the Meta-analysis of Observational Studies in Epidemiology (MOOSE) group consensus statement for conducting and reporting the results of systematic review. PubMed and EMBASE were searched for the observational studies which reported predictive utility of qSOFA score for predicting mortality in patients with suspected or proven infection with the following search words: 'qSOFA', 'q-SOFA', 'quick-SOFA', 'Quick Sequential Organ Failure Assessment', 'quick SOFA'. Sensitivity, specificity, area under receiver operating characteristic (ROC) curves with 95% confidence interval (CI) of qSOFA and SIRS criteria for predicting in-hospital mortality was collected for each study and a 2 × 2 table was created for each study.

RESULTS

Data of 406 802 patients from 45 observational studies were included in this meta-analysis. Pooled sensitivity (95% CI) and specificity (95% CI) of qSOFA ≥2 for predicting mortality in patients who were not in an intensive care unit (ICU) was 0.48 (0.41-0.55) and 0.83 (0.78-0.87), respectively. Pooled sensitivity (95% CI) of qSOFA ≥2 for predicting mortality in patients (both ICU and non-ICU settings) with suspected infection was 0.56 (0.47-0.65) and pooled specificity (95% CI) was 0.78 (0.71-0.83).

CONCLUSION

qSOFA has been found to be a poorly sensitive predictive marker for in-hospital mortality in hospitalized patients with suspected infection. It is reasonable to recommend developing another scoring system with higher sensitivity to identify high-risk patients with infection.

Bioconversion of fish solid waste into PHB using Bacillus subtilis based submerged fermentation process

Currently, one of the major problem affecting the world is solid waste management, predominantly petroleum-based plastic and fish solid waste (FSW). However, it is very difficult to reduce the consumption of plastic as well as fish products, but it is promising to convert FSW to biopolymer to reduce eco-pollution. On account of that, the bioconversion of FSW extract to polyhydroxybutyrate (PHB) was undertaken by using Bacillus subtilis (KP172548). Under optimized conditions, 1.62 g/L of PHB has been produced by the bacterium. The purified compound was further characterized by advanced analytical technologies to elucidate its chemical structure. Results indicated that the biopolymer was found to be PHB, the most common homopolymer of polyhydroxyalkanoates (PHAs). This is the first report demonstrating the efficacy of B. subtilis to utilize FSW extract to produce biopolymer. The biocompatibility of the PHB against murine macrophage cell line RAW264.7 demonstrated that, it was comparatively less toxic, favourable for surface attachment and proliferation in comparison with poly-lactic acid (PLA) and commercially available PHB. Thus, further exploration is highly indispensable to use FSW extract as a substrate for production of PHB at pilot scale.

3-Amino-4-aminoximidofurazan derivatives: small molecules possessing antimicrobial and antibiofilm activity against Staphylococcus aureus and Pseudomonas aeruginosa

AIM

The therapeutic treatment of microbial infections involving biofilm becomes quite challenging because of its increasing antibiotic resistance capacities. Towards this direction, in the present study we have evaluated the antibiofilm property of synthesized 3-amino-4-aminoximidofurazan compounds having polyamine skeleton. These derivatives were synthesized by incorporating furazan and biguanide moieties.

METHODS AND RESULTS

Different 3-amino-4-aminoximidofurazan derivatives (PI1-4) were synthesized via protic acid catalysis and subsequently characterized by (1) H NMR and (13) C NMR spectra, recorded at 400 and 100 MHz respectively. We have tested the antimicrobial and antibiofilm activities of these synthetic derivatives (PI1-4) against both Staphylococcus aureus and Pseudomonas aeruginosa. The compounds so tested were also compared with standard antibiotics namely Tobramycin (Ps. aeruginosa) and Azithromycin (Staph. aureus) which were used as a positive control in all experimental sets. All these compounds (PI1-4) exhibited moderate to significant antimicrobial activities against both micro-organisms wherein compound PI3 showed maximum activity. Biofilm inhibition of both micro-organisms was then evaluated by crystal violet and safranin staining, estimation of biofilm total protein and microscopy methods using sub-MIC dose of these compounds. Results showed that all compounds executed anti biofilm activity against both Staph. aureus and Ps. aeruginosa wherein compound PI3 exhibited maximum activity. In relation with microbial biofilm inhibition, we have observed reduction in bacterial motility, proteolytic activity and secreted exo-polysaccharide (EPS) from both Staph. aureus and Ps. aeruginosa when they were grown in presence of these compounds. While addressing the issue of toxicity on host, we have observed that these molecules exhibited minimum level of R.B.C degradation.

CONCLUSION

These findings establish the antibacterial and anti biofilm properties of 3-amino-4-aminoximidofurazan derivatives (PI1-4).

SIGNIFICANCE AND IMPACT OF THE STUDY

Therefore, our current findings demonstrate that 3-amino-4-aminoximidofurazan derivatives (PI1-4) may hold promise to be effective biofilm and microbial inhibitors that may be clinically significant.

Multilevel programming in Cu/NiO y /NiO x /Pt unipolar resistive switching devices

The application of a NiO y /NiO x bilayer in resistive switching (RS) devices with x > y was studied for its ability to achieve reliable multilevel cell (MLC) characteristics. A sharp change in resistance brought about by sweeping the voltage, along with an improved on/off ratio (>10(3)) and endurance (10(4)) were achieved in the bilayer structure as compared to the single NiO x layer devices. Moreover, it was found that nonvolatile and stable resistance levels, especially the multiple low-resistance states of Cu/NiO y /NiO x /Pt memory devices, could be controlled by varying the compliance current. All the multilevel resistance states of the Cu/NiO y /NiO x /Pt bilayer devices were stable for up to 500 consecutive dc switching cycles, as compared to the Cu/NiO x /Pt single layer devices. The temperature-dependent variation of the high and low resistance states of both the bilayer and single layer devices was further investigated to elucidate the charge conduction mechanism. Finally, based on a detailed analysis of the experimental results, comparisons of the possible models for RS in bilayer and single layer memory devices have also been discussed.

Proximate Kitaev quantum spin liquid behaviour in a honeycomb magnet

Quantum spin liquids (QSLs) are topological states of matter exhibiting remarkable properties such as the capacity to protect quantum information from decoherence. Whereas their featureless ground states have precluded their straightforward experimental identification, excited states are more revealing and particularly interesting owing to the emergence of fundamentally new excitations such as Majorana fermions. Ideal probes of these excitations are inelastic neutron scattering experiments. These we report here for a ruthenium-based material, α-RuCl3, continuing a major search (so far concentrated on iridium materials) for realizations of the celebrated Kitaev honeycomb topological QSL. Our measurements confirm the requisite strong spin-orbit coupling and low-temperature magnetic order matching predictions proximate to the QSL. We find stacking faults, inherent to the highly two-dimensional nature of the material, resolve an outstanding puzzle. Crucially, dynamical response measurements above interlayer energy scales are naturally accounted for in terms of deconfinement physics expected for QSLs. Comparing these with recent dynamical calculations involving gauge flux excitations and Majorana fermions of the pure Kitaev model, we propose the excitation spectrum of α-RuCl3 as a prime candidate for fractionalized Kitaev physics.

Site preference of NH3-adsorption on Co, Pt and CoPt surfaces: the role of charge transfer, magnetism and strain

Oxidation of Co at the surface poses a major problem in the cyclable use of CoPt, a cost-effective catalyst for proton exchange membrane fuel cells.

Diversity of killer cell immunoglobulin-like receptor genes in the Bengali population of northern West Bengal, India

The Indian Subcontinent exhibits extensive diversity in its culture, religion, ethnicity and linguistic heritage, which symbolizes extensive genetic variations within the populations. The highly polymorphic Killer cell Immunoglobulin-like Receptor (KIR) family plays an important role in tracing genetic differentiation in human population. In this study, we aimed to analyse the KIR gene polymorphism in the Bengali population of northern West Bengal, India. To our knowledge, this is the first report on the KIR gene polymorphism in the Bengalis of West Bengal, India. Herein, we have studied the distribution of 14 KIR genes (KIR3DL1-3DL3, KIR2DL1-2DL5, KIR2DS1-2DS5 AND KIR3DS1) and two pseudogenes (KIR3DP1 and 2DP1) in the Bengalis. Apart from the framework genes (KIR2DL4, 3DL2, 3DL3 and 3DP1), which are present in all the individuals, the gene frequencies of other KIR genes varied between 0.34 and 0.88. Moreover, upon comparing the KIR polymorphism of the Bengalis with the available published data of other world populations, it has been found that the Indo-European-speaking Bengalis from the region share both Dravidian and Indo-Aryan gene pool with considerable influences of mongoloid and European descents. Furthermore, evidences from previously published data on human leucocyte antigen and Y-chromosome haplogroup diversity support the view. Our results will help to understand the genetic background of the Bengali population, in illustrating the population migration events in the eastern and north-eastern part of India, in explaining the extensive genetic admixture amongst the different linguistic groups of the region and also in KIR-related disease researches.

Displacive-type ferroelectricity from magnetic correlations within spin-chain

Observation of ferroelectricity among non-d(0) systems, which was believed for a long time an unrealistic concept, led to various proposals for the mechanisms to explain the same (i.e. magnetically induced ferroelectricity) during last decade. Here, we provide support for ferroelectricity of a displacive-type possibly involving magnetic ions due to short-range magnetic correlations within a spin-chain, through the demonstration of magnetoelectric coupling in a Haldane spin-chain compound Er2BaNiO5 well above its Néel temperature of (TN = ) 32 K. There is a distinct evidence for electric polarization setting in near 60 K around which there is an evidence for short-range magnetic correlations from other experimental methods. Raman studies also establish a softening of phonon modes in the same temperature (T) range and T-dependent x-ray diffraction (XRD) patterns also reveal lattice parameters anomalies. Density-functional theory based calculations establish a displacive component (similar to d(0)-ness) as the root-cause of ferroelectricity from (magnetic) NiO6 chain, thereby offering a new route to search for similar materials near room temperature to enable applications.

Selective accumulation of aluminum in cerebral arteries in Alzheimer's disease (AD)

Once biologically available aluminum bypasses gastrointestinal and blood-brain barriers, this environmentally-abundant neurotoxin has an exceedingly high affinity for the large pyramidal neurons of the human brain hippocampus. This same anatomical region of the brain is also targeted by the earliest evidence of Alzheimer's disease (AD) neuropathology. The mechanism for the selective targeting and transport of aluminum into the hippocampus of the human brain is not well understood. In an effort to improve our understanding of a pathological aluminum entry system into the brain, this study examined the aluminum content of 8 arteries that supply blood to the hippocampus, including the aorta and several cerebral arteries. In contrast to age-matched controls, in AD patients we found a gradient of increasing aluminum concentration from the aorta to the posterior cerebral artery that supplies blood to the hippocampus. Primary cultures of human brain endothelial cells were found to have an extremely high affinity for aluminum when compared to other types of brain cells. Together, these results suggest for the first time that endothelial cells that line the cerebral vasculature may have biochemical attributes conducive to binding and targeting aluminum to selective anatomical regions of the brain, such as the hippocampus, with potential downstream pro-inflammatory and pathogenic consequences.

A gas-jet transport and catcher technique for on-line production of radioactive ion beams using an electron cyclotron resonance ion-source

Radioactive ion beams (RIB) have been produced on-line, using a gas-jet recoil transport coupled Electron Cyclotron Resonance (ECR) ion-source at the VECC-RIB facility. Radioactive atoms∕molecules carried through the gas-jet were stopped in a catcher placed inside the ECR plasma chamber. A skimmer has been used to remove bulk of the carrier gas at the ECR entrance. The diffusion of atoms∕molecules through the catcher has been verified off-line using stable isotopes and on-line through transmission of radioactive reaction products. Beams of (14)O (71 s), (42)K (12.4 h), (43)K (22.2 h), and (41)Ar (1.8 h) have been produced by bombarding nitrogen and argon gas targets with proton and alpha particle beams from the K130 cyclotron at VECC. Typical measured intensity of RIB at the separator focal plane is found to be a few times 10(3) particles per second (pps). About 3.2 × 10(3) pps of 1.4 MeV (14)O RIB has been measured after acceleration through a radiofrequency quadrupole linac. The details of the gas-jet coupled ECR ion-source and RIB production experiments are presented along with the plans for the future.