Evaluation of the efficacy of tongue swab and saliva as samples for testing COVID-19 infection in symptomatic cases in comparison with nasopharyngeal swab.

Introduction. COVID-19 caused by SARS CoV-2 continues to be a major health concern globally. Methods for detection of the disease are necessary for public health efforts to monitor the spread of this disease as well as for detecting the emergence of new variants.Gap statement. Collection of Nasopharyngeal swab (NPS), the gold standard sample for the detection of COVID-19 infection by RT-qPCR is invasive and requires the expertise of a trained medical provider. This highlights the need for validating less invasive samples that can be self-collected without the need for trained medical provider.Aim. To validate saliva and tongue swab as potential samples for the diagnosis of COVID-19.Methodology. Adult and paediatric cases who had acute influenza like illness were enrolled in the study. The study involved comparison of Nucleic Acid Amplification Tests (NAAT) results for the detection of COVID-19 obtained by using saliva and tongue swab with that of NPS.Result and Conclusion. The sensitivity and specificity of saliva as sample for COVID-19 detection were found to be 71 and 88% respectively whereas those of tongue swab as sample were 78 and 90 %. Further validation was based on the positive and negative predictive values, the likelihood ratio, agreement percentage and the kappa statistic. The findings of the study point towards tongue swab and saliva as suitable alternative samples for the diagnosis of COVID-19 with a slightly higher accuracy and agreement for tongue swab than saliva. However considering the fatality of COVID-19, they are better suited for mass screening of people than for diagnosis.

Mean rate of progression of visual fields in patients with primary open-angle glaucoma and ocular hypertension attending a tertiary care center in South India - A prospective cohort study using FORUM® Glaucoma Workplace software.

Purpose: To find out the mean rate of progression (MROP) of visual fields (VF) in patients with primary open-angle glaucoma (POAG) and ocular hypertension (OHT) using FORUM® Glaucoma Workplace. Methods: Two hundred and one eyes of 105 patients were included in this prospective cohort study. Patients with POAG and OHT were recruited, and VF analysis with 24-2 and or 10-2 was done using SITA standard strategy in Zeiss Humphrey Visual Field Analyzer (HFA). All the previous VFs were identified from FORUM software, and the baseline indices were recorded from the first reliable VF analysis. The present VF analysis was compared to the previous one using FORUM software, and the rate of progression (ROP) in VF was obtained by Guided Progression Analysis. Results: MROP of VF in the POAG group was - 0.085 dB/year, ranging from -2.8 to 2.8 dB/year with a standard deviation (SD) of 0.69. In the OHT group, the MROP of VF was -0.003 dB/year, ranging from - 0.8 to 0.5 dB/year with an SD of 0.27. The MROP of VF in medically treated eyes with POAG was -0.14 dB/year with an SD of 0.61 and in surgically treated eyes was -0.02 dB/year with an SD of 0.78. The overall baseline mean VF index (VFI) was 83.19% and the final mean VFI was 79.80%. There was a statistically significant decrease in the mean VFI value from baseline to the final visit (P-value 0.0005). Conclusion: The mean ROP of VF in the POAG group was -0.085 dB/year and in the OHT group was - 0.003 dB/year.

Molecular dynamics of mismatch detection-How MutS uses indirect readout to find errors in DNA.

The mismatch repair protein MutS safeguards genomic integrity by finding and initiating repair of basepairing errors in DNA. Single-molecule studies show MutS diffusing on DNA, presumably scanning for mispaired/unpaired bases, and crystal structures show a characteristic "mismatch-recognition" complex with DNA enclosed within MutS and kinked at the site of error. But how MutS goes from scanning thousands of Watson-Crick basepairs to recognizing rare mismatches remains unanswered, largely because atomic-resolution data on the search process are lacking. Here, 10 µs all-atom molecular dynamics simulations of Thermus aquaticus MutS bound to homoduplex DNA and T-bulge DNA illuminate the structural dynamics underlying the search mechanism. MutS-DNA interactions constitute a multistep mechanism to check DNA over two helical turns for its 1) shape, through contacts with the sugar-phosphate backbone, 2) conformational flexibility, through bending/unbending engineered by large-scale motions of the clamp domain, and 3) local deformability, through basepair destabilizing contacts. Thus, MutS can localize a potential target by indirect readout due to lower energetic costs of bending mismatched DNA and identify a site that distorts easily due to weaker base stacking and pairing as a mismatch. The MutS signature Phe-X-Glu motif can then lock in the mismatch-recognition complex to initiate repair.

Outcomes of bleb needling in primary glaucoma: A prospective interventional study in a South Indian population.

Purpose: This study was conducted to assess the outcomes of bleb needling for the treatment of failure of filtration surgeries in primary glaucoma with a follow-up of six months. Methods: This prospective interventional study included patients with primary glaucoma who underwent trabeculectomy or combined glaucoma and cataract surgery with failed or failing bleb after six weeks of surgery and less than two years. A comprehensive examination including best-corrected visual acuity (BCVA), intraocular pressure (IOP) measurement, gonioscopy, slit-lamp examination, and bleb morphology grading was done. Selected patients underwent a subconjunctival bleb needling with mitomycin C (MMC) (dose 0.2 mg/ml). Postoperatively, patients were followed up on the first, third, and sixth months and were assessed with respect to IOP, need for antiglaucoma medication (AGM), and complications. Results: Sixty eyes of 59 patients were included. Preoperatively, 33.3% of patients were on one AGM, whereas postoperatively at the third month 51.7% and at the sixth month 50% of patients were on no AGM. There was a statistically significant decrease in IOP (P < 0.001) from preoperative (mean: 23.8 ± 7.86 mmHg) to postoperative first month (mean: 19.8 ± 9.08 mmHg), third month (mean: 17.4 ± 5.4 mmHg) and sixth month (mean 16.6 ± 4.39). According to the defined criteria in the current study, we achieved 22 (37.9%) successes, 31 qualified successes (53.4%), and 5 (8.6%) failures. Univariate regression analysis showed a higher failure rate among younger age groups. Gender, laterality, and intraoperative complications were not significant statistically. Conclusion: Bleb needling is a safe and effective procedure for the treatment of failed filtration surgeries.

What are mycorrhizal traits?

Traits are inherent properties of organisms, but how are they defined for organismal networks such as mycorrhizal symbioses? Mycorrhizal symbioses are complex and diverse belowground symbioses between plants and fungi that have proved challenging to fit into a unified and coherent trait framework. We propose an inclusive mycorrhizal trait framework that classifies traits as morphological, physiological, and phenological features that have functional implications for the symbiosis. We further classify mycorrhizal traits by location - plant, fungus, or the symbiosis - which highlights new questions in trait-based mycorrhizal ecology designed to charge and challenge the scientific community. This new framework is an opportunity for researchers to interrogate their data to identify novel insights and gaps in our understanding of mycorrhizal symbioses.

Sagacious Perceptive on Marburg Virus Foregrounding the Recent Findings: A Critical Review.

Infectious diseases are defined as a group of diseases caused by any infecting microorganism which are highly potent to severely affect human life. The end can vary from critical infection to mortality. Most infectious diseases are reported with a rapid rate of transmission. Marburg virus disease is a kind of infectious viral disease usually manifested as hemorrhagic fever. The latest reported case of Marburg virus disease confirmed by WHO was on 6th August 2021 in the south-western province of Guinea. Marburg virus disease exhibit similar manifestations to that of infection with the Ebola virus. Though not widely spread to emerge as a pandemic, Marburg virus disease remains a serious threat to human life. This review emphasizes the novel current facts determined through various studies related to Marburg virus infection. From these promising theories, the review tries to put forward the importance of various study conclusions, which are likely to have a major impact on the health sector in the near future.

Medication-Adherence and Management of Risk Factors for Secondary Prevention of Stroke Using Smartphone-Based Application: Protocol for MAMORs-Randomized Controlled Trial.

Background: In LMICs, the medication adherence and risk factor control are suboptimal in the post-stroke follow-up period. With shortage of physicians, smartphone-based interventions can help stroke survivors in secondary stroke prevention. Objectives: We aim to validate a digital innovative technology-based intervention to improve the awareness, medication adherence, control of risk factors through timely intervention of physician among the stroke survivors. Methods: MAMOR is a smartphone-based application to improve the stroke awareness by heath education materials, reminders to timely adherence of medication, alerts on control of risk factors, video files, and timely physician intervention. The study will involve development of the app using contextual research (Delphi qualitative method) followed by a randomized, single center, double arm-controlled trial with 1:1 assignment. The app will be evaluated over a period of 6 months with a target to enroll 192 participants. Process evaluation will be conducted. The sample size was calculated as 192, considering medication adherence of 43.8%, 20% increase in medication adherence by app, power of 80%, and 10% loss to follow-up. Results: The primary outcome will be medication adherence, changes in the lifestyle and behavioral and control of vascular risk factors. The secondary outcome will include vascular events and functional outcome. Conclusion: This study will be one among the few studies for secondary prevention of stroke through digital technology innovation in LMICs with resource constraints. The evidences generated from this study will provide translational evidence for other similar settings for stroke survivors.

World symbiosis day webinar - when living together is a win-win.

The following information is intended for those who were unable to attend the first webinar of the International Symbiosis Society (ISS) on - 'When living together is a win-win' - a celebration of 'World Symbiosis Day' on 30 July 2020. The objective of the webinar was to disseminate information about the Society, to gather feedback, and to encourage the audience to join the Society. This introduction presents a summary of the webinar, highlighting the keynote presentations, the panel discussion, the journal Symbiosis, and the next ISS conference to be held in Lyon in 2022. In addition, we report on the discussions and feedback from participants that were collected through polls and other aspects of the webinar.

Recurrent mismatch binding by MutS mobile clamps on DNA localizes repair complexes nearby.

DNA mismatch repair (MMR), the guardian of the genome, commences when MutS identifies a mismatch and recruits MutL to nick the error-containing strand, allowing excision and DNA resynthesis. Dominant MMR models posit that after mismatch recognition, ATP converts MutS to a hydrolysis-independent, diffusive mobile clamp that no longer recognizes the mismatch. Little is known about the postrecognition MutS mobile clamp and its interactions with MutL. Two disparate frameworks have been proposed: One in which MutS-MutL complexes remain mobile on the DNA, and one in which MutL stops MutS movement. Here we use single-molecule FRET to follow the postrecognition states of MutS and the impact of MutL on its properties. In contrast to current thinking, we find that after the initial mobile clamp formation event, MutS undergoes frequent cycles of mismatch rebinding and mobile clamp reformation without releasing DNA. Notably, ATP hydrolysis is required to alter the conformation of MutS such that it can recognize the mismatch again instead of bypassing it; thus, ATP hydrolysis licenses the MutS mobile clamp to rebind the mismatch. Moreover, interaction with MutL can both trap MutS at the mismatch en route to mobile clamp formation and stop movement of the mobile clamp on DNA. MutS's frequent rebinding of the mismatch, which increases its residence time in the vicinity of the mismatch, coupled with MutL's ability to trap MutS, should increase the probability that MutS-MutL MMR initiation complexes localize near the mismatch.

Trace metal distribution in the sediment cores of mangrove ecosystems along northern Kerala coast, south-west coast of India.

Core sediment samples were collected from five mangrove ecosystems along northern Kerala coast (Kunjimangalam: S1, Pazhayangadi: S2, Pappinissery: S3, Thalassery: S4, and Kadalundi: S5) to assess the status of heavy metal pollution. S1 recorded comparatively lower metal concentration at surface (except Pb) due to low organic content and sandy texture, while the reverse was true for S3. Higher metal contents were recorded at S5 (0-5 cm), which was attributed to its unique biogeochemical behavior. Enrichment factor and geoaccumulation index indicated moderate enrichment for Cd, and the pollution load index revealed progressive deterioration of sediment quality at S5 (0-5 cm). There was no harmful effect of trace metals on biological community (except Ni) according to Sediment Quality Guidelines. Major processes controlling trace metal accumulation in these systems are diagenetic processes, precipitation of heavy metals as sulfides, and the presence of Fe, Mn-oxy hydroxides, which act as adsorption sites for other metals.

Mismatch Recognition by Saccharomyces cerevisiae Msh2-Msh6: Role of Structure and Dynamics.

The mismatch repair (MMR) pathway maintains genome integrity by correcting errors such as mismatched base pairs formed during DNA replication. In MMR, Msh2-Msh6, a heterodimeric protein, targets single base mismatches and small insertion/deletion loops for repair. By incorporating the fluorescent nucleoside base analog 6-methylisoxanthopterin (6-MI) at or adjacent to a mismatch site to probe the structural and dynamic elements of the mismatch, we address how Msh2-Msh6 recognizes these mismatches for repair within the context of matched DNA. Fluorescence quantum yield and rotational correlation time measurements indicate that local base dynamics linearly correlate with Saccharomyces cerevisiae Msh2-Msh6 binding affinity where the protein exhibits a higher affinity (KD ≤ 25 nM) for mismatches that have a significant amount of dynamic motion. Energy transfer measurements measuring global DNA bending find that mismatches that are both well and poorly recognized by Msh2-Msh6 experience the same amount of protein-induced bending. Finally, base-specific dynamics coupled with protein-induced blue shifts in peak emission strongly support the crystallographic model of directional binding, in which Phe 432 of Msh6 intercalates 3' of the mismatch. These results imply an important role for local base dynamics in the initial recognition step of MMR.

The ATPase mechanism of UvrA2 reveals the distinct roles of proximal and distal ATPase sites in nucleotide excision repair.

The UvrA2 dimer finds lesions in DNA and initiates nucleotide excision repair. Each UvrA monomer contains two essential ATPase sites: proximal (P) and distal (D). The manner whereby their activities enable UvrA2 damage sensing and response remains to be clarified. We report three key findings from the first pre-steady state kinetic analysis of each site. Absent DNA, a P2ATP-D2ADP species accumulates when the low-affinity proximal sites bind ATP and enable rapid ATP hydrolysis and phosphate release by the high-affinity distal sites, and ADP release limits catalytic turnover. Native DNA stimulates ATP hydrolysis by all four sites, causing UvrA2 to transition through a different species, P2ADP-D2ADP. Lesion-containing DNA changes the mechanism again, suppressing ATP hydrolysis by the proximal sites while distal sites cycle through hydrolysis and ADP release, to populate proximal ATP-bound species, P2ATP-Dempty and P2ATP-D2ATP. Thus, damaged and native DNA trigger distinct ATPase site activities, which could explain why UvrA2 forms stable complexes with UvrB on damaged DNA compared with weaker, more dynamic complexes on native DNA. Such specific coupling between the DNA substrate and the ATPase mechanism of each site provides new insights into how UvrA2 utilizes ATP for lesion search, recognition and repair.

Urbanization and biodiversity of arbuscular mycorrhizal fungi: The case study of Delhi, India / Urbanización y biodiversidad de hongos micorrízicos arbusculares -Caso de estudio de Delhi, India

Abstract Increasing urbanisation is widely associated with decline in biodiversity of all forms. The aim of the present study was to answer two questions: (i) Does rapid urbanization in Delhi (India) affect biodiversity of arbuscular mycorrhizal (AM) fungi? (ii) If so, how? We measured the AM fungal diversity at nine sites located in Delhi forests, which had different types of urban usage in terms of heavy vehicular traffic pollution, littering, defecation and recreational activities. The study revealed a significant decrease in AM fungal diversity (alpha diversity) and abundance measured as spore density, biovolume, mean infection percentage (MIP) in roots, soil hyphal length and easily extractable glomalin related soluble proteins (EE-GRSP) at polluted sites. Non-metric multidimensional scaling (NMDS) and nested PERMANOVA, revealed significant differences in AM fungal community structure which could be correlated with variations in soil moisture, temperature, pH, carbon, and nitrogen and phosphorus levels. BEST (biota and environmental matching) analysis of biological and environmental samples revealed that soil temperature and moisture accounted for 47.6 % of the total variations in the samples. The study demonstrated how different forms of human activities in urban ecosystems of Delhi are detrimental to the diversity and abundance of AM fungi.(AU)

Resumen El incremento en la urbanización está ampliamente asociado con una disminución de la biodiversidad de todas las formas. El objetivo del presente estudio fue responder dos preguntas: (i) ¿Afecta la urbanización rápida en Delhi (India) la biodiversidad de hongos micorrízicos arbusculares (MA)?, y (ii) si es así, ¿Cómo? Medimos la diversidad de hongos MA en nueve sitios ubicados en los bosques de Delhi, los cuales tenían diferentes tipos de uso urbano en términos de contaminación por alto tráfico vehicular, basura, defecación y actividades recreacionales. El estudio reveló una disminución significativa en la diversidad de hongos MA (diversidad alfa) y abundancia medida como densidad de esporas, biovolumen, porcentaje medio de infección (PMI) en raíces, longitud de las hifas del suelo y glomalina fácilmente extraible relacionada con proteínas solubles (EE-GRSP) en sitios contaminados. Análisis de escalamiento multidimensional no métrico (NMDS) y PERMANOVA anidados revelaron diferencias significativas en la estructura de hongos MA, que puede estar relacionada con la variación en humedad, temperatura, pH y niveles de carbono, nitrógeno y fósforo del suelo. El análisis BEST (biota y correspondencia ambiental) de muestras biológicas y ambientales mostró que la temperatura y humedad del suelo explican un 47.6 % del total de la variación en las muestras. Este estudio demostró cómo las diferentes actividades humanas en ecosistemas urbanos de Delhi son perjudiciales para la diversidad y abundancia de hongos MA.(AU)

MutSγ-Induced DNA Conformational Changes Provide Insights into Its Role in Meiotic Recombination.

In many organisms, MutSγ plays a role in meiotic recombination, facilitating crossover formation between homologous chromosomes. Failure to form crossovers leads to improper segregation of chromosomes and aneuploidy, which in humans result in infertility and birth defects. To improve current understanding of MutSγ function, this study investigates the binding affinities and structures of MutSγ in complex with DNA substrates that model homologous recombination intermediates. For these studies, we overexpressed and isolated from Escherichia coli the yeast MutSγ protein Saccharomyces cerevisiae (Sc) Msh4-Msh5. Sc Msh4-Msh5 binds Holliday junction (HJ)-like substrates, 3' overhangs, single-stranded (ss) forks, and the displacement loop with nanomolar affinity. The weakest binding affinities are detected for an intact duplex and open-junction construct. Similar to the human protein, Sc Msh4-Msh5 exhibits the highest affinity for the HJ with a Kd < 0.4 nM in solution. Energy-transfer experiments further demonstrate that DNA structure is modulated by the binding interaction with the largest changes associated with substrates containing an ss end. Upon binding, Sc Msh4-Msh5 displaces the ss away from the duplex in most of the ss-containing intermediates, potentially enabling the binding of RPA and other proteins. In the case of the junction-like intermediates, Msh4-Msh5 binding either stabilizes the existing stacked structure or induces formation of the stacked X conformation. Significantly, we find that upon binding, Msh4-Msh5 stacks an open-junction construct to the same extent as the standard junction. Stabilization of the junction in the stacked conformation is generally refractory to branch migration, which is consistent with a potential role for MutSγ to stabilize HJs and prevent branch migration until resolution by MutLγ. The different binding modalities observed suggest that Msh4-Msh5 not only binds to and stabilizes stacked junctions but also participates in meiotic recombination before junction formation through the stabilization of single-end invasion intermediates.

Coordinated protein and DNA conformational changes govern mismatch repair initiation by MutS.

MutS homologs identify base-pairing errors made in DNA during replication and initiate their repair. In the presence of adenosine triphosphate, MutS induces DNA bending upon mismatch recognition and subsequently undergoes conformational transitions that promote its interaction with MutL to signal repair. In the absence of MutL, these transitions lead to formation of a MutS mobile clamp that can move along the DNA. Previous single-molecule FRET (smFRET) studies characterized the dynamics of MutS DNA-binding domains during these transitions. Here, we use protein-DNA and DNA-DNA smFRET to monitor DNA conformational changes, and we use kinetic analyses to correlate DNA and protein conformational changes to one another and to the steps on the pathway to mobile clamp formation. The results reveal multiple sequential structural changes in both MutS and DNA, and they suggest that DNA dynamics play a critical role in the formation of the MutS mobile clamp. Taking these findings together with data from our previous studies, we propose a unified model of coordinated MutS and DNA conformational changes wherein initiation of mismatch repair is governed by a balance of DNA bending/unbending energetics and MutS conformational changes coupled to its nucleotide binding properties.

Missed cleavage opportunities by FEN1 lead to Okazaki fragment maturation via the long-flap pathway.

RNA-DNA hybrid primers synthesized by low fidelity DNA polymerase α to initiate eukaryotic lagging strand synthesis must be removed efficiently during Okazaki fragment (OF) maturation to complete DNA replication. In this process, each OF primer is displaced and the resulting 5'-single-stranded flap is cleaved by structure-specific 5'-nucleases, mainly Flap Endonuclease 1 (FEN1), to generate a ligatable nick. At least two models have been proposed to describe primer removal, namely short- and long-flap pathways that involve FEN1 or FEN1 along with Replication Protein A (RPA) and Dna2 helicase/nuclease, respectively. We addressed the question of pathway choice by studying the kinetic mechanism of FEN1 action on short- and long-flap DNA substrates. Using single molecule FRET and rapid quench-flow bulk cleavage assays, we showed that unlike short-flap substrates, which are bound, bent and cleaved within the first encounter between FEN1 and DNA, long-flap substrates can escape cleavage even after DNA binding and bending. Notably, FEN1 can access both substrates in the presence of RPA, but bending and cleavage of long-flap DNA is specifically inhibited. We propose that FEN1 attempts to process both short and long flaps, but occasional missed cleavage of the latter allows RPA binding and triggers the long-flap OF maturation pathway.

Positioning the 5'-flap junction in the active site controls the rate of flap endonuclease-1-catalyzed DNA cleavage.

Flap endonucleases catalyze cleavage of single-stranded DNA flaps formed during replication, repair, and recombination and are therefore essential for genome processing and stability. Recent crystal structures of DNA-bound human flap endonuclease (hFEN1) offer new insights into how conformational changes in the DNA and hFEN1 may facilitate the reaction mechanism. For example, previous biochemical studies of DNA conformation performed under non-catalytic conditions with Ca2+ have suggested that base unpairing at the 5'-flap:template junction is an important step in the reaction, but the new structural data suggest otherwise. To clarify the role of DNA changes in the kinetic mechanism, we measured a series of transient steps, from substrate binding to product release, during the hFEN1-catalyzed reaction in the presence of Mg2+ We found that whereas hFEN1 binds and bends DNA at a fast, diffusion-limited rate, much slower Mg2+-dependent conformational changes in DNA around the active site are subsequently necessary and rate-limiting for 5'-flap cleavage. These changes are reported overall by fluorescence of 2-aminopurine at the 5'-flap:template junction, indicating that local DNA distortion (e.g. disruption of base stacking observed in structures), associated with positioning the 5'-flap scissile phosphodiester bond in the hFEN1 active site, controls catalysis. hFEN1 residues with distinct roles in the catalytic mechanism, including those binding metal ions (Asp-34 and Asp-181), steering the 5'-flap through the active site and binding the scissile phosphate (Lys-93 and Arg-100), and stacking against the base 5' to the scissile phosphate (Tyr-40), all contribute to these rate-limiting conformational changes, ensuring efficient and specific cleavage of 5'-flaps.

Linchpin DNA-binding residues serve as go/no-go controls in the replication factor C-catalyzed clamp-loading mechanism.

DNA polymerases depend on circular sliding clamps for processive replication. Clamps must be loaded onto primer-template DNA (ptDNA) by clamp loaders that open and close clamps around ptDNA in an ATP-fueled reaction. All clamp loaders share a core structure in which five subunits form a spiral chamber that binds the clamp at its base in a twisted open form and encloses ptDNA within, while binding and hydrolyzing ATP to topologically link the clamp and ptDNA. To understand how clamp loaders perform this complex task, here we focused on conserved arginines that might play a central coordinating role in the mechanism because they can alternately contact ptDNA or Walker B glutamate in the ATPase site and lie close to the clamp loader-clamp-binding interface. We mutated Arg-84, Arg-88, and Arg-101 in the ATPase-active B, C, and D subunits of Saccharomyces cerevisiae replication factor C (RFC) clamp loader, respectively, and assessed the impact on multiple transient events in the reaction: proliferating cell nuclear antigen (PCNA) clamp binding/opening/closure/release, ptDNA binding/release, and ATP hydrolysis/product release. The results show that these arginines relay critical information between the PCNA-binding, DNA-binding, and ATPase sites at all steps of the reaction, particularly at a checkpoint before RFC commits to ATP hydrolysis. Moreover, their actions are subunit-specific with RFC-C Arg-88 serving as an accelerator that enables rapid ATP hydrolysis upon contact with ptDNA and RFC-D Arg-101 serving as a brake that confers specificity for ptDNA as the correct substrate for loading PCNA.