Investigating the potent TOPO IIα inhibitors in breast cancer through the study of computational drug discovery research approaches

Breast cancer (BC) is the second-leading cause of cancer after lung cancer. The disease has affected millions of people and resulted in many deaths. In the metastasis of breast cancer cells, Topoisomerase IIα plays a vital role. Therefore, this investigation aims to identify potential flavonoid compounds against BC by inhibiting this enzyme at an early stage. Based on previous studies, we selected and screened several plant-derived flavonoid compounds with potential anti-breast cancer activity using PyRx 0.8 and Schrodinger applications for preliminary molecular docking: the highest docking scores of Myricetin (-11.6 kcal/mol) and Quercetin (-10.0 kcal/mol). Next, we evaluated the top four compounds on the Way2Drug server to complete the cytotoxicity evaluation, which demonstrated anti-cancer and anti-breast cancer activity in various cell lines. According to pharmacokinetics studies, four compounds exhibited outstanding values and functioned similar to drug-like molecules. Moreover, Myricetin, Quercetin, and Morin displayed the highest number of hydrogen bonds, with the corresponding receptor forming residues asn120, thr147, and lys168. The protein-ligand complexes were validated using the Desmond simulator, and their data were compared to the anti-breast cancer drug Doxorubicin. In the simulation analysis, various parameters were evaluated, including RMSD, RMSF, Rg, SASA, MolSA, PSA, and hydrogen bond interaction. Finally, validated our dynamic simulation result with MM-GBSA operation, and Myricetin and Quercetin had the greatest score of -72.74344651, -66.66771823 kcal/mol, which is outstanding than the control drug. Hence, the computational research approach determined that Myricetin, Quercetin, and Morin could be industrially developed for the alternative treatment of breast cancer following additional confirmation from animal and cell line studies.

Lipoma of the gastrointestinal tract: a tertiary care centre experience

INTRODUCTION

Gastrointestinal (GI) lipomas are rare; however, they are frequent enough to be considered in the differential diagnosis of gut tumours. Here, we present our experience with GI lipomas managed at our institute over the last three years.

METHODS

This is a retrospective cohort study of patients with GI lipomas managed between January, 2020 and April, 2023 at a tertiary care centre. Clinical presentation, location, and details of surgical procedure were analysed.

RESULTS

Ten patients were included, six of whom had lipoma in the colon, one in the stomach, and one each in the duodenum, jejunum, and ileum. The mean age at the time of presentation was 48.8 years (range, 19-77 years), and strong male preponderance (4:1) was noted. Preoperative diagnosis of lipoma on cross-sectional imaging was possible in all patients. All patients were symptomatic and were managed surgically.

CONCLUSIONS

While GI lipomas are generally considered to be indolent and benign tumours, they can potentially lead to severe complications. The utilisation of computed tomography and magnetic resonance imaging has brought about a significant transformation in diagnosing this condition, enabling preoperative identification in most cases. The surgery offers a definitive treatment with minimal risk of postoperative complications.

Erratum: Search for Cosmic-Ray Boosted Sub-GeV Dark Matter Using Recoil Protons at Super-Kamiokande [Phys. Rev. Lett. 130, 031802 (2023)]

This corrects the article DOI: 10.1103/PhysRevLett.130.031802.

Measurements of neutrino oscillation parameters from the T2K experiment using 3.6×1021 protons on target

The T2K experiment presents new measurements of neutrino oscillation parameters using 19.7 ( 16.3 ) × 10 20 protons on target (POT) in (anti-)neutrino mode at the far detector (FD). Compared to the previous analysis, an additional 4.7 × 10 20 POT neutrino data was collected at the FD. Significant improvements were made to the analysis methodology, with the near-detector analysis introducing new selections and using more than double the data. Additionally, this is the first T2K oscillation analysis to use NA61/SHINE data on a replica of the T2K target to tune the neutrino flux model, and the neutrino interaction model was improved to include new nuclear effects and calculations. Frequentist and Bayesian analyses are presented, including results on sin 2 θ 13 and the impact of priors on the δ CP measurement. Both analyses prefer the normal mass ordering and upper octant of sin 2 θ 23 with a nearly maximally CP-violating phase. Assuming the normal ordering and using the constraint on sin 2 θ 13 from reactors, sin 2 θ 23 = 0 . 561 - 0.032 + 0.021 using Feldman-Cousins corrected intervals, and Δ m 32 2 = 2 . 494 - 0.058 + 0.041 × 10 - 3 eV 2 using constant Δ χ 2 intervals. The CP-violating phase is constrained to δ CP = - 1 . 97 - 0.70 + 0.97 using Feldman-Cousins corrected intervals, and δ CP = 0 , π is excluded at more than 90% confidence level. A Jarlskog invariant of zero is excluded at more than 2 σ credible level using a flat prior in δ CP , and just below 2 σ using a flat prior in sin δ CP . When the external constraint on sin 2 θ 13 is removed, sin 2 θ 13 = 28 . 0 - 6.5 + 2.8 × 10 - 3 , in agreement with measurements from reactor experiments. These results are consistent with previous T2K analyses.

Modulation of Cystatin F in Human Macrophages Impacts Cathepsin-Driven Killing of Multidrug-Resistant Mycobacterium tuberculosis

Tuberculosis (TB) treatment relies primarily on 70-year-old drugs, and prophylaxis suffers from the lack of an effective vaccine. Among the 10 million people exhibiting disease symptoms yearly, 450,000 have multidrug or extensively drug-resistant (MDR or XDR) TB. A greater understanding of host and pathogen interactions will lead to new therapeutic interventions for TB eradication. One of the strategies will be to target the host for better immune bactericidal responses against the TB causative agent Mycobacterium tuberculosis (Mtb). Cathepsins are promising targets due to their manipulation of Mtb with consequences such as decreased proteolytic activity and improved pathogen survival in macrophages. We recently demonstrated that we could overcome this enzymatic blockade by manipulating protease inhibitors such as cystatins. Here, we investigate the role of cystatin F, an inhibitor that we showed previously to be strongly upregulated during Mtb infection. Our results indicate that the silencing of cystatin F using siRNA increase the proteolytic activity of cathepsins S, L, and B, significantly impacting pathogen intracellular killing in macrophages. Taken together, these indicate the targeting of cystatin F as a potential adjuvant therapy for TB, including MDR and XDR-TB.

ESAT-6 a Major Virulence Factor of Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb), the causative agent of human tuberculosis (TB), is one of the most successfully adapted human pathogens. Human-to-human transmission occurs at high rates through aerosols containing bacteria, but the pathogen evolved prior to the establishment of crowded populations. Mtb has developed a particular strategy to ensure persistence in the host until an opportunity for transmission arises. It has refined its lifestyle to obviate the need for virulence factors such as capsules, flagella, pili, or toxins to circumvent mucosal barriers. Instead, the pathogen uses host macrophages, where it establishes intracellular niches for its migration into the lung parenchyma and other tissues and for the induction of long-lived latency in granulomas. Finally, at the end of the infection cycle, Mtb induces necrotic cell death in macrophages to escape to the extracellular milieu and instructs a strong inflammatory response that is required for the progression from latency to disease and transmission. Common to all these events is ESAT-6, one of the major virulence factors secreted by the pathogen. This narrative review highlights the recent advances in understanding the role of ESAT-6 in hijacking macrophage function to establish successful infection and transmission and its use as a target for the development of diagnostic tools and vaccines.

Development of Chitosan Particles Loaded with siRNA for Cystatin C to Control Intracellular Drug-Resistant Mycobacterium tuberculosis

The golden age of antibiotics for tuberculosis (TB) is marked by its success in the 1950s of the last century. However, TB is not under control, and the rise in antibiotic resistance worldwide is a major threat to global health care. Understanding the complex interactions between TB bacilli and their host can inform the rational design of better TB therapeutics, including vaccines, new antibiotics, and host-directed therapies. We recently demonstrated that the modulation of cystatin C in human macrophages via RNA silencing improved the anti-mycobacterial immune responses to Mycobacterium tuberculosis infection. Available in vitro transfection methods are not suitable for the clinical translation of host-cell RNA silencing. To overcome this limitation, we developed different RNA delivery systems (DSs) that target human macrophages. Human peripheral blood-derived macrophages and THP1 cells are difficult to transfect using available methods. In this work, a new potential nanomedicine based on chitosan (CS-DS) was efficiently developed to carry a siRNA-targeting cystatin C to the infected macrophage models. Consequently, an effective impact on the intracellular survival/replication of TB bacilli, including drug-resistant clinical strains, was observed. Altogether, these results suggest the potential use of CS-DS in adjunctive therapy for TB in combination or not with antibiotics.

HIV/Mtb Co-Infection: From the Amplification of Disease Pathogenesis to an “Emerging Syndemic”

Human immunodeficiency virus (HIV) and Mycobacterium tuberculosis (Mtb) are pathogens responsible for millions of new infections each year; together, they cause high morbidity and mortality worldwide. In addition, late-stage HIV infection increases the risk of developing tuberculosis (TB) by a factor of 20 in latently infected people, and even patients with controlled HIV infection on antiretroviral therapy (ART) have a fourfold increased risk of developing TB. Conversely, Mtb infection exacerbates HIV pathogenesis and increases the rate of AIDS progression. In this review, we discuss this reciprocal amplification of HIV/Mtb coinfection and how they influence each other’s pathogenesis. Elucidating the infectious cofactors that impact on pathogenesis may open doors for the design of new potential therapeutic strategies to control disease progression, especially in contexts where vaccines or the sterile clearance of pathogens are not effectively available.

Substitution of Ca2+ and changes in the H-bond network near the oxygen-evolving complex of photosystem II

Ca²⁺, which provides binding sites for ligand water molecules W3 and W4 in the Mn₄CaO₅ cluster, is a prerequisite for O₂ evolution in photosystem II (PSII). We report structural changes in the H-bond network and the catalytic cluster itself upon the replacement of Ca²⁺ with other alkaline earth metals, using a quantum mechanical/molecular mechanical approach. The small radius of Mg²⁺ makes W3 donate an H-bond to D1-Glu189 in Mg²⁺-PSII. If an additional water molecule binds at the large surface of Ba²⁺, it donates H-bonds to D1-Glu189 and the ligand water molecule at the dangling Mn, altering the H-bond network. The potential energy profiles of the H-bond between D1-Tyr161 (TyrZ) and D1-His190 and the interconversion between the open- and closed-cubane S₂ conformations remain substantially unaltered upon the replacement of Ca²⁺. Remarkably, the O5⋯Ca²⁺ distance is shortest among all O5⋯metal distances irrespective of the radius being larger than that of Mg²⁺. Furthermore, Ca²⁺ is the only alkaline earth metal that equalizes the O5⋯metal and O2⋯metal distances and facilitates the formation of the symmetric cubane structure.

Search for Cosmic-Ray Boosted Sub-GeV Dark Matter Using Recoil Protons at Super-Kamiokande

We report a search for cosmic-ray boosted dark matter with protons using the 0.37  megaton×years data collected at Super-Kamiokande experiment during the 1996-2018 period (SKI-IV phase). We searched for an excess of proton recoils above the atmospheric neutrino background from the vicinity of the Galactic Center. No such excess is observed, and limits are calculated for two reference models of dark matter with either a constant interaction cross section or through a scalar mediator. This is the first experimental search for boosted dark matter with hadrons using directional information. The results present the most stringent limits on cosmic-ray boosted dark matter and exclude the dark matter-nucleon elastic scattering cross section between 10^{-33}cm^{2} and 10^{-27}cm^{2} for dark matter mass from 1  MeV/c^{2} to 300  MeV/c^{2}.

Liposomal Delivery of Saquinavir to Macrophages Overcomes Cathepsin Blockade by Mycobacterium tuberculosis and Helps Control the Phagosomal Replicative Niches

Mycobacterium tuberculosis is able to establish a chronic colonization of lung macrophages in a controlled replication manner, giving rise to a so-called latent infection. Conversely, when intracellular bacteria undergo actively uncontrolled replication rates, they provide the switch for the active infection called tuberculosis to occur. Our group found that the pathogen is able to manipulate the activity of endolysosomal enzymes, cathepsins, directly at the level of gene expression or indirectly by regulating their natural inhibitors, cystatins. To provide evidence for the crucial role of cathepsin manipulation for the success of tuberculosis bacilli in their intracellular survival, we used liposomal delivery of saquinavir. This protease inhibitor was previously found to be able to increase cathepsin proteolytic activity, overcoming the pathogen induced blockade. In this study, we demonstrate that incorporation in liposomes was able to increase the efficiency of saquinavir internalization in macrophages, reducing cytotoxicity at higher concentrations. Consequently, our results show a significant impact on the intracellular killing not only to reference and clinical strains susceptible to current antibiotic therapy but also to multidrug- and extensively drug-resistant (XDR) Mtb strains. Altogether, this indicates the manipulation of cathepsins as a fine-tuning strategy used by the pathogen to survive and replicate in host cells.

Impact of air pollutants on COVID-19 transmission: a study over different metropolitan cities in India

India is affected strongly by the Coronavirus and within a short period, it becomes the second-highest country based on the infected case. Earlier, there was an indication of the impact of pollution on COVID-19 transmission from a few studies with early COVID-19 data. The study of the effect of pollution on COVID-19 in Indian metropolitan cities is ideal due to the high level of pollution and COVID-19 transmission in these cities. We study the impact of different air pollutants on the spread of coronavirus in different cities in India. A correlation is studied with daily confirmed COVID-19 cases with a daily mean of ozone, particle matter (PM) in size ≤ 10 μ m, carbon monoxide, sulfur dioxide, and nitrogen dioxide of different cities. It is found that particulate matter concentration decreases during the nationwide lockdown period and the air quality index improves for different Indian regions. A correlation between the daily confirmed cases with particulate matter (PM2.5 and PM10 both) is observed. The air quality index also shows a positive correlation with the daily confirmed cases for most of the metropolitan Indian cities. The correlation study also indicates that different air pollutants may have a role in the spread of the virus.

Spatial localization of cathepsins: Implications in immune activation and resolution during infections

Cathepsins were first described, as endolysosomal proteolytic enzymes in reference to the organelles where they degrade the bulk of endogenous and exogenous substrates in a slightly acidic environment. These substrates include pathogens internalized via endocytosis and/or marked for destruction by autophagy. However, the role of cathepsins during infection far exceeds that of direct digestion of the pathogen. Cathepsins have been extensively investigated in the context of tumour associated immune cells and chronic inflammation. Several cathepsin-dependent immune responses develop in the endocytic pathway while others take place in the cytosol, the nucleus, or in the extracellular space. In this review we highlight the spatial localization of cathepsins and their implications in immune activation and resolution pathways during infection.

Impact of climate on COVID-19 transmission: A study over Indian states

Coronavirus Disease-2019 (COVID-19) started in Wuhan province of China in November 2019 and within a short time, it was declared as a worldwide pandemic by World Health Organisation due to the very fast worldwide spread of the virus. There are a few studies that look for the correlation with infected individuals and different environmental parameters using early data of COVID-19 but there is no study so far that deals with the variation of effective reproduction number and environmental factors. Effective reproduction number is the driving parameter of the spread of a pandemic and it is important to study the effect of various environmental factors on effective reproduction number to understand the effect of those factors on the spread of the virus. We have used time-dependent models to investigate the variation of different time-dependent driving parameters of COVID-19 like effective reproduction number and contact rate using data from India as a test case. India is a large population country that is highly affected due to the COVID-19 pandemic and has a wide span of different temperature and humidity regions and is ideal for such study. We have studied the impact of temperature and humidity on the spread of the virus of different Indian states using time-dependent epidemiological models SIRD, and SEIRD for a long time scale. We have used a linear regression method to look for any dependency between the effective reproduction number with the relative humidity, absolute humidity, and temperature. The effective reproduction number shows a negative correlation with both relative and absolute humidity for most of the Indian states, which are statistically significant. This implies that relative and absolute humidity may have an important role in the variation of effective reproduction number. Most of the states (six out of ten) show a positive correlation while two (out of ten) show a negative correlation between effective reproduction number and average air temperature for both SIRD and SEIRD models.

Release of a Proton and Formation of a Low-Barrier Hydrogen Bond between Tyrosine D and D2-His189 in Photosystem II

In photosystem II (PSII), the second-lowest oxidation state (S₁) of the oxygen-evolving Mn₄CaO₅ cluster is the most stable, as the radical form of the redox-active D2-Tyr160 is considered to be a candidate that accepts an electron from the lowest oxidation state (S₀) in the dark. Using quantum mechanical/molecular mechanical calculations, we investigated the redox potential (E _m) of TyrD and its H-bond partner, D2-His189. The potential energy profile indicates that the release of a proton from the TyrD...D2-His189 pair leads to the formation of a low-barrier H-bond. The E _m depends on the H⁺ position along the low-barrier H-bond, e.g., 680 mV when the H⁺ is at the D2-His189 moiety and 800 mV when the H⁺ is at the TyrD moiety, which can explain why TyrD mediates both the S₀ to S₁ oxidation and the S₂ to S₁ reduction.

Natural Product-Based Potential Therapeutic Interventions of Pulmonary Fibrosis

Pulmonary fibrosis (PF) is a disease-refractive lung condition with an increased rate of mortality. The potential factors causing PF include viral infections, radiation exposure, and toxic airborne chemicals. Idiopathic PF (IPF) is related to pneumonia affecting the elderly and is characterized by recurring scar formation in the lungs. An impaired wound healing process, defined by the dysregulated aggregation of extracellular matrix components, triggers fibrotic scar formation in the lungs. The potential pathogenesis includes oxidative stress, altered cell signaling, inflammation, etc. Nintedanib and pirfenidone have been approved with a conditional endorsement for the management of IPF. In addition, natural product-based treatment strategies have shown promising results in treating PF. In this study, we reviewed the recently published literature and discussed the potential uses of natural products, classified into three types—isolated active compounds, crude extracts of plants, and traditional medicine, consisting of mixtures of different plant products—in treating PF. These natural products are promising in the treatment of PF via inhibiting inflammation, oxidative stress, and endothelial mesenchymal transition, as well as affecting TGF-β-mediated cell signaling, etc. Based on the current review, we have revealed the signaling mechanisms of PF pathogenesis and the potential opportunities offered by natural product-based medicine in treating PF.

Requirement of Chloride for the Downhill Electron Transfer Pathway from the Water-Splitting Center in Natural Photosynthesis

In photosystem II (PSII), Cl^- is a prerequisite for the second flash-induced oxidation of the Mn₄CaO₅ cluster (the S₂ to S₃ transition). We report proton transfer from the substrate water molecule via D1-Asp61 and electron transfer via redox-active D1-Tyr161 (TyrZ) to the chlorophyll pair in Cl^--depleted PSII using a quantum mechanical/molecular mechanical approach. The low-barrier H-bond formation between the substrate water molecule and D1-Asp61 remained unaffected upon the depletion of Cl^-. However, the binding site, D2-Lys317, formed a salt bridge with D1-Asp61, leading to the inhibition of the subsequent proton transfer. Remarkably, the redox potential (E_m) of S₂/S₃ increased significantly, making electron transfer from S₂ to TyrZ energetically uphill, as observed in Ca²⁺-depleted PSII. The uphill electron transfer pathway was induced by the significant increase in E_m(S₂/S₃) caused by the loss of charge compensation for D2-Lys317 upon the depletion of Cl^-, whereas it was induced by the significant decrease in E_m(TyrZ) caused by the rearrangement of the water molecules at the Ca²⁺ binding moiety upon the depletion of Ca²⁺.

Effect of 2021 assembly election in India on COVID-19 transmission

India is one of the countries in the world which is badly affected by the COVID-19 second wave. Assembly election in four states and a union territory of India was taken place during March-May 2021 when the COVID-19 second wave was close to its peak and affected a huge number of people. We studied the impact of assembly election on the effective contact rate and the effective reproduction number of COVID-19 using different epidemiological models like SIR, SIRD, and SEIR. We also modeled the effective reproduction number for all election-bound states using different mathematical functions. We separately studied the case of all election-bound states and found all the states showed a distinct increase in the effective contact rate and the effective reproduction number during the election-bound time and just after that compared to pre-election time. States, where elections were conducted in single-phase, showed less increase in the effective contact rate and the reproduction number. The election commission imposed extra measures from the first week of April 2021 to restrict big campaign rallies, meetings, and different political activities. The effective contact rate and the reproduction number showed a trend to decrease for few states due to the imposition of the restrictions. We also compared the effective contact rate, and the effective reproduction number of all election-bound states and the rest of India and found all the parameters related to the spread of virus for election-bound states are distinctly high compared to the rest of India.

Requirement of Chloride for the Downhill Electron Transfer Pathway from the Water-Splitting Center in Natural Photosynthesis

In photosystem II (PSII), Cl^- is a prerequisite for the second flash-induced oxidation of the Mn₄CaO₅ cluster (the S₂ to S₃ transition). We report proton transfer from the substrate water molecule via D1-Asp61 and electron transfer via redox-active D1-Tyr161 (TyrZ) to the chlorophyll pair in Cl^--depleted PSII using a quantum mechanical/molecular mechanical approach. The low-barrier H-bond formation between the substrate water molecule and D1-Asp61 remained unaffected upon the depletion of Cl^-. However, the binding site, D2-Lys317, formed a salt bridge with D1-Asp61, leading to the inhibition of the subsequent proton transfer. Remarkably, the redox potential (E_m) of S₂/S₃ increased significantly, making electron transfer from S₂ to TyrZ energetically uphill, as observed in Ca²⁺-depleted PSII. The uphill electron transfer pathway was induced by the significant increase in E_m(S₂/S₃) caused by the loss of charge compensation for D2-Lys317 upon the depletion of Cl^-, whereas it was induced by the significant decrease in E_m(TyrZ) caused by the rearrangement of the water molecules at the Ca²⁺ binding moiety upon the depletion of Ca²⁺.

Modulation of Cystatin C in Human Macrophages Improves Anti-Mycobacterial Immune Responses to Mycobacterium tuberculosis Infection and Coinfection With HIV

Tuberculosis owes its resurgence as a major global health threat mostly to the emergence of drug resistance and coinfection with HIV. The synergy between HIV and Mycobacterium tuberculosis (Mtb) modifies the host immune environment to enhance both viral and bacterial replication and spread. In the lung immune context, both pathogens infect macrophages, establishing favorable intracellular niches. Both manipulate the endocytic pathway in order to avoid destruction. Relevant players of the endocytic pathway to control pathogens include endolysosomal proteases, cathepsins, and their natural inhibitors, cystatins. Here, a mapping of the human macrophage transcriptome for type I and II cystatins during Mtb, HIV, or Mtb-HIV infection displayed different profiles of gene expression, revealing cystatin C as a potential target to control mycobacterial infection as well as HIV coinfection. We found that cystatin C silencing in macrophages significantly improves the intracellular killing of Mtb, which was concomitant with an increased general proteolytic activity of cathepsins. In addition, downmodulation of cystatin C led to an improved expression of the human leukocyte antigen (HLA) class II in macrophages and an increased CD4⁺ T-lymphocyte proliferation along with enhanced IFN-γ secretion. Overall, our results suggest that the targeting of cystatin C in human macrophages represents a promising approach to improve the control of mycobacterial infections including multidrug-resistant (MDR) TB.

Role of redox-inactive metals in controlling the redox potential of heterometallic manganese-oxido clusters

Photosystem II (PSII) contains Ca2+, which is essential to the oxygen-evolving activity of the catalytic Mn4CaO5 complex. Replacement of Ca2+ with other redox-inactive metals results in a loss/decrease of oxygen-evolving activity. To investigate the role of Ca2+ in this catalytic reaction, we investigate artificial Mn3[M]O2 clusters redox-inactive metals  [M] ([M]  = Mg2+, Ca2+, Zn2+, Sr2+, and Y3+), which were synthesized by Tsui et al. (Nat Chem 5:293, 2013). The experimentally measured redox potentials (Em) of these clusters are best described by the energy of their highest occupied molecular orbitals. Quantum chemical calculations showed that the valence of metals predominantly affects Em(MnIII/IV), whereas the ionic radius of metals affects Em(MnIII/IV) only slightly.

Proton exit pathways surrounding the oxygen evolving complex of photosystem II

Photosystem II allows water to be the primary electron source for the photosynthetic electron transfer chain. Water is oxidized to dioxygen at the Oxygen Evolving Complex (OEC), a Mn₄CaO₅ inorganic core embedded on the lumenal side of PSII. Water-filled channels surrounding the OEC must bring in substrate water molecules, remove the product protons to the lumen, and may transport the product oxygen. Three water-filled channels, denoted large, narrow, and broad, extend from the OEC towards the aqueous surface more than 15 Å away. However, the role of each pathway in the transport in and out of the OEC is yet to be established. Here, we combine Molecular Dynamics (MD), Multi Conformation Continuum Electrostatics (MCCE) and Network Analysis to compare and contrast the three potential proton transfer paths. Hydrogen bond network analysis shows that near the OEC the waters are highly interconnected with similar free energy for hydronium at all locations. The paths diverge as they move towards the lumen. The water chain in the broad channel is better connected than in the narrow and large channels, where disruptions in the network are observed approximately 10 Å from the OEC. In addition, the barrier for hydronium translocation is lower in the broad channel. Thus, a proton released from any location on the OEC can access all paths, but the likely exit to the lumen passes through PsbO via the broad channel.

Two Distinct Oxygen-Radical Conformations in the X-ray Free Electron Laser Structures of Photosystem II

We report the existence of two distinct oxygen-radical-containing Mn₄CaO_5/6 conformations with short O···O bonds in the crystal structures of the oxygen-evolving enzyme photosystem II (PSII), obtained using an X-ray free electron laser (XFEL). A short O···O distance of <2.3 Å between the O4 site of the Mn₄CaO₅ complex and the adjacent water molecule (W539) in the proton-conducting O4-water chain was observed in the second flash-induced (2F) XFEL structure (2F-XFEL), which may correspond to S₃. By use of a quantum mechanical/molecular mechanical approach, the OH^• formation at W539 and the short O4···O_W539 distance (<2.3 Å) were reproduced in S₂ and S₃ with reduced Mn1(III), which lacks the additional sixth water molecule O6. As the O^•- formation at O6 and the short O5···O6 distance (1.9 Å) have been reported in another 2F-XFEL structure with reduced Mn4(III), two distinct oxygen-radical conformations exist in the 2F-XFEL crystals.

Repurposing Saquinavir for Host-Directed Therapy to Control Mycobacterium Tuberculosis Infection

Despite the available antibiotics, tuberculosis (TB) has made its return since the 90’s of the last century as a global threat mostly due to co-infection with HIV, to the emergence of drug resistant strains and the lack of an effective vaccine. Host-directed strategies could be exploited to improve treatment efficacy, contain drug-resistant strains, improve immune responses and reduce disease severity. Macrophages in the lungs are often found infected with Mycobacterium tuberculosis (Mtb) and/or with HIV. The long-term survival of lung macrophages infected with Mtb or with HIV, together with their ability to produce viral particles, especially during TB, makes these niches major contributors to the pathogenicity of the infection. Among the available drugs to control HIV infection, protease inhibitors (PIs), acting at post-integrational stages of virus replication cycle, are the only drugs able to interfere with virus production and release from macrophages during chronic infection. For Mtb we recently found that the pathogen induces a general down-regulation of lysosomal proteases, helping bacteria to establish an intracellular niche in macrophages. Here we found that the PI saquinavir, contrary to ritonavir, is able to induce an increase of endolysosomal proteases activity especially of cathepsin S in Mtb infected macrophages and during co-infection with HIV. Our results indicate that saquinavir treatment of infected macrophages led not only to a significant intracellular killing of Mtb but also: (i) to an improved expression of the HLA class II antigen presentation machinery at the cell surface; (ii) to increased T-lymphocyte priming and proliferation; and (iii) to increased secretion of IFN-γ. All together the results indicate saquinavir as a potential host directed therapy for tuberculosis.

The Nature of the Short Oxygen-Oxygen Distance in the Mn4CaO6 Complex of Photosystem II Crystals

The O···O distance for a typical H-bond is ∼2.8 Å, whereas the radiation-damage-free structures of photosystem II (PSII), obtained using the X-ray free electron laser (XFEL), shows remarkably short O···O distances of ∼2 Å in the oxygen-evolving Mn₄CaO_5/6 complex. Herein, we report the protonation/oxidation states of the short O···O atoms in the XFEL structures using a quantum mechanical/molecular mechanical approach. The O5···O6 distance of 1.9 Å is reproduced only when O6 is an unprotonated O radical (O^•-) with Mn(IV)₃Mn(III), i.e., the S₃ state. The potential energy profile shows a barrier-less energy minimum region when O5···O6 = 1.90-2.05 Å (O^•- ↓) or 2.05-2.20 Å (O^•- ↑). Formation of such a short O5···O6 distance is not possible when O6 is OH^- with Mn(IV)₄. In the case in which the O5···O6 distance is 1.9 Å, it seems likely that the O radical species exists in the oxygen-evolving complex of the XFEL-S₃ crystals.

Characterization of the Burkholderia cenocepacia J2315 Surface-Exposed Immunoproteome

Infections by the Burkholderia cepacia complex (Bcc) remain seriously life threatening to cystic fibrosis (CF) patients, and no effective eradication is available. A vaccine to protect patients against Bcc infections is a highly attractive therapeutic option, but none is available. A strategy combining the bioinformatics identification of putative surface-exposed proteins with an experimental approach encompassing the “shaving” of surface-exposed proteins with trypsin followed by peptide identification by liquid chromatography and mass spectrometry is here reported. The methodology allowed the bioinformatics identification of 263 potentially surface-exposed proteins, 16 of them also experimentally identified by the “shaving” approach. Of the proteins identified, 143 have a high probability of containing B-cell epitopes that are surface-exposed. The immunogenicity of three of these proteins was demonstrated using serum samples from Bcc-infected CF patients and Western blotting, validating the usefulness of this methodology in identifying potentially immunogenic surface-exposed proteins that might be used for the development of Bcc-protective vaccines.

1048 Prevalence Of Positional Obstructive Sleep Apnea (OSA) In Patients With OSA-COPD Overlap Syndrome

Introduction

Positional OSA (non-supine apnea-hypopnea index [AHI] &lt; 5 events/hr) is present in 30% of patients with OSA. We demonstrated that in patients with OSA- COPD overlap syndrome the AHI inversely correlated with the degree of gas trapping, suggesting a stabilizing effect on the upper airway. We hypothesized that sleep position would be less important, resulting in a lower prevalence of positional OSA.

Methods

Patients underwent a polysomnogram that demonstrated OSA (AHI &gt; 5 events/hr). To confirm COPD, patients had spirometry performed and a chest computed tomography for measurements of percent gas trapping.

Results

Sixteen patients [6 (38%) males, 55±7 years/old, FEV1 1.2±0.5 L, FEV1 % Predicted 45±19%, FVC 2.3±0.8 L, FVC % Predicted 69±20%, FEV1/FVC 51±12%, BMI 33±9 kg/m2)] were diagnosed with OSA (AHI 15±12 events/hour). Four patients (25%) had positional OSA (AHI 13±6 events/hr, non-supine AHI 1±1 event/hr) compared to 12 patients who were non-positional [AHI 16±13 events/hr (p=0.95)]. There was no difference in age [52±8 and 56±7 yrs (p=0.3)] or severity of obstruction in those with and without positional OSA [FEV1 1.4±4 L and 1.1±0.5 L, (p=0.3), FEV1 % predicted 50±17% and 44±20%, (p=0.7), FVC 2.9±0.8 L and 2.1±0.8 L (p=0.1), FVC % predicted 78±21% and 66±20%, (p=0.3), and FEV1/FVC 50±11% and 51±12%, (p=0.8), respectively]. However, patients with positional OSA were less heavy than those with non-positional OSA [BMI 23±3 and 37±8 kg/m2, respectively (p=0.005)]. Finally, there was no difference in the CT-Derived % Gas Trapping in those with and without positional OSA [48±37% and 36±25%, (p=0.6), respectively].

Conclusion

The prevalence of positional OSA in patients with OSA-COPD overlap is similar to OSA patients without COPD. Despite the presence of obstructive disease and gas trapping that may affect upper airway stability, other factors including body position and BMI remain important determinants for developing OSA in patients with COPD.

Support

R01-HL089856, R01-HL089897

0567 Hypoxic Burden and Apnea-Hypopnea Duration in Patients with Positional Obstructive Sleep Apnea

Introduction

Recently, the measurement of the hypoxic burden and apnea-hypopnea duration has been shown to correlate with mortality in patients with obstructive sleep apnea (OSA). We hypothesized that in patients with mild positional OSA (apnea-hypopnea index [AHI] &lt; 5 events/hr in the non-supine position) the hypoxic burden would be increased and apnea-hypopnea duration shortened and similar to patients with non-positional OSA.

Methods

Fourteen patients with positional OSA and 24 patients non-positional OSA with similar severity of OSA based on the respiratory event index (REI) were included. All patients had a home sleep apnea test for suspected OSA. The hypoxic burden was calculated by the multiplication of REI and the mean area under the desaturation curves.

Results

Thirty-eight patients [12 (35%) males, 50±12 yrs, BMI 35±7 kg/m2, Epworth Sleepiness Scale (ESS) 11±8, REI 10±3 events/hr, apnea-hypopnea duration 19±4 sec, mean SaO2 94±2%, lowest SaO2 79±8%, % total sleep time (TST) SaO2 &lt; 90% 11±16%, hypoxic burden 30±17 %min/hr] completed the study. Fourteen patients [9 (64%) males, 46±14 yrs, BMI 31±6 kg/m2, ESS 7±5, REI 9±3 events/hr, mean SaO2 94±2%, lowest SaO2 81±6%, %TST SaO2 &lt; 90% 4±6%] had positional OSA (supine REI 16±7 events/hr, non-supine REI 3±1 events/hr) and 24 patients had non-positional OSA [3 (13%) males, 52±10 yrs, BMI 38±7 kg/m2, ESS 12±9, REI 10±3 events/hr, mean SaO2 94±2%, lowest SaO2 77±9%, %TST SaO2 &lt; 90% 14±19%]. The hypoxic burden was elevated in both the positional and non-positional OSA patients with no difference between the groups (26±19 %min/hr and 32±15 %min/hr, respectively, p=0.13). The apnea-hypopnea duration was similar in positional and non-positional OSA patients (20±3 sec and 18±4 sec, respectively, p=0.08 sec).

Conclusion

In patients with mild positional OSA the hypoxic burden, which has been associated with cardiovascular mortality, is elevated and similar to patients with non-positional OSA.

Support

None

0610 Prevalence of Positional Obstructive Sleep Apnea Based on 3% Vs 4% Oxygen Desaturation Using Home Sleep Apnea Testing

Introduction

Approximately 30% of patient with obstructive sleep apnea (OSA) have positional OSA [non-supine apnea-hypopnea index (AHI) &lt; 5 events/hr]. However, the prevalence is based on variable definitions for hypopneas related to the degree of oxygen desaturation. In addition, use of a home sleep apnea test (HSAT) to identify positional OSA is limited. We hypothesized that in patients evaluated with an HSAT, using a definition for hypopneas based on 4% compared to 3% oxygen desaturation will significantly decrease the percentage diagnosed with positional OSA.

Methods

Fourteen patients with positional OSA based on a non-supine respiratory event index (REI) &lt; 5 events/hr were included. The initial diagnosis was determined based on a hypopnea definition of ≥ 3% oxygen desaturation. The studies were reanalyzed using a hypopnea definition of ≥ 4% oxygen desaturation.

Results

Fourteen patients [9 (64%) males, 46±14 yrs, BMI 31±6 kg/m2, ESS 7±5, REI 9±3 events/hr, mean SaO2 94±2%, lowest SaO2 81±6%, %TST SaO2 &lt; 90% 4±6%] were identified with positional OSA (supine REI 16±7 events/hr, non-supine REI 3±1 events/hr) using a hypopneas definition of ≥ 3% oxygen desaturation. When reanalyzed using a hypopnea ≥ 4% oxygen desaturation there was a significant decrease in the REI to 7±2 events/hr (p&lt;0.001). Three patients (21%) no longer were considered to have OSA. These patients were younger (32±14 vs. 50±11yrs, p=0.03) and had less severe OSA (REI 6±1 vs. 9±3 events/hr (p=0.04), but there was no difference in BMI (32±11 vs. 31±5 kg/m2, p=0.9) or mean and lowest SaO2 (96±0.4 vs. 94±2%, p=0.13, and 82±8 vs. 81±6%, p=0.9, respectively).

Conclusion

In patients with mild positional OSA, using a hypopnea definition of at least 4% vs. 3% oxygen desaturation on a HSAT will have a significant effect on the overall REI and often exclude patients who would otherwise be treated for OSA.

Support

None.

Cardiological society of India document on safety measure during echo evaluation of cardiovascular disease in the time of COVID-19

An echocardiographic investigation is one of the key modalities of diagnosis in cardiology. There has been a rising presence of cardiological comorbidities in patients positive for COVID-19. Hence, it is becoming extremely essential to look into the correct safety precautions, healthcare professionals must take while conducting an echo investigation. The decision matrix formulated for conducting an echocardiographic evaluation is based on presence or absence of cardiological comorbidity vis-à-vis positive, suspected or negative for COVID-19. The safety measures have been constructed keeping in mind the current safety precautions by WHO, CDC and MoHFW, India.

Cardiological Society of India: Document on acute MI care during COVID-19

The unprecedented and rapidly spreading Coronavirus Disease-19 (COVID-19) pandemic has challenged public health care systems globally. Based on worldwide experience, India has initiated a nationwide lockdown to prevent the exponential surge of cases. During COVID-19, management of cardiovascular emergencies like acute Myocardial Infarction (MI) may be compromised. Cardiological Society of India (CSI) has ventured in this moment of crisis to evolve a consensus document for care of acute MI. However, this care should be individualized, based on local expertise and governmental advisories.

Redox Potential of the Oxygen-Evolving Complex in the Electron Transfer Cascade of Photosystem II

In photosystem II (PSII), water oxidation occurs in the Mn₄CaO₅ cluster with the release of electrons via the redox-active tyrosine (TyrZ) to the reaction-center chlorophylls (P_D1/P_D2). Using a quantum mechanical/molecular mechanical approach, we report the redox potentials (E_m) of these cofactors in the PSII protein environment. The E_m values suggest that the Mn₄CaO₅ cluster, TyrZ, and P_D1/P_D2 form a downhill electron transfer pathway. E_m for the first oxidation step, E_m(S₀/S₁), is uniquely low (730 mV) and is ∼100 mV lower than that for the second oxidation step, E_m(S₁/S₂) (830 mV) only when the O4 site of the Mn₄CaO₅ cluster is protonated in S₀. The O4-water chain, which directly forms a low-barrier H-bond with the Mn₄CaO₅ cluster and mediates proton-coupled electron transfer in the S₀ to S₁ transition, explains why the second lowest oxidation state, S₁, is the most stable and S₀ is converted to S₁ even in the dark.

Redox potentials along the redox-active low-barrier H-bonds in electron transfer pathways

Local proton transfer along redox-active low-barrier H-bonds can alter the driving force or electronic coupling for electron transfer, as the redox potential values depend on the H⁺ position in low-barrier H-bonds.

Epidemiological and clinical profile of Influenza A(H1N1) pdm09 in Odisha, eastern India

Epidemic of flu is highly contagious and it spreads through air. In 2009 H1N1 influenza virus emerged after reassortment of North American TRIG and Eurasia Avian like virus of swine and started epidemic in Mexico. The first cases were reported from Hyderabad city on 16th May 2009 in India that spread rapidly within a short span of time. During this period large population of Odisha situated at the eastern side of India was also affected and incidences of H1N1 cases were recorded through state Government surveillance system. In this study real time RT-PCR based diagnosis was conducted for the throat swabs collected from suspected H1N1 cases in Odisha during 2009–2017. A total of 2872 throat swabs were received from 23 different Government and private hospitals and 21.1% positivity was confirmed. The disease affected mostly 46–60 years age group, males (50.6%) being more affected. The clinical features had shown that fever with cough (89.6%) was the most common symptom followed by shortness of breath (72.7%). Post monsoon was the peak season in which most of the cases were reported. Neurological signs, pregnancy, diabetes and hypertension were found to be risk factors for H1N1. The case fatality rate (CFR) was 15%.

Anti-diabetic effect of Oyster Mushroom mediates through increased AMP-activated protein kinase (AMPK) and cyclic AMP-response element binding (CREB) protein in Type 2 Diabetic model Rats

AMP-activated protein kinase (AMPK) and c-AMP-response element binding protein (CREB) are found to be important proteins in metabolic system. AMPK has become the focus as a novel therapeutic target for the treatment of metabolic syndromes. Oyster mushroom is traditionally used as remedy of diabetes and hypertension. The present study aims to observe the stimulation of AMPK and CREB in streptozotocin-induced diabetic model rats through Oyster mushroom administration. Long Evan’s rats were used to create type 2 model diabetic rats through intraperitoneal injection of streptozotocin at 90mg/kg body weight of 48hr old pups. Rats were divided into three groups: diabetic control rats, glibenclamide treated diabetic rats (positive control) and mushroom treated diabetic rats (experimental group). Mushroom was administered orally at a dose of 1.25g/kg body weight in semisolid forms. After five weeks rats were sacrificed, serum and tissues were collected for future analysis. Glucose was measured using glucose-oxidase method, lipid profile by enzymaticcolorimetric method. Proteins from different tissues were extracted using RIPA cell lysis buffer, AMPK and CREB were identified using western blot and immuno-precipitation techniques. A significant decreased of fasting glucose was found after 35 days of experiment when it compared with control diabetic rats (M ± SD, mmol/l, Diabetic control group: 8.0±1.1; Mushroom treated diabetic group: 6.4±1.0; p=0.021). Glibenclamide treated diabetic rats have also shown decreased fasting glucose compared to control diabetic rats. In paired ‘t’ test analysis, it has been found that serum fasting glucose level was significantly decreased on 35th day compared the 0 day in both mushroom treated group (p=0.027) and in glibenclamide treated group (p=0.005). Serum TG level was decreased on 35th day compared to 0day in mushroom treated diabetic model rats only (M±SD, mg/dl, 0 day: 84±13; 35th day: 61±6, p=0.002). No significant changes of cholesterol, HDL and LDL were noticed in the experimental groups following treatment with mushroom. Western blot analyses have shown increased band intensity of AMPK and p-CREB in mushroom treated diabetic model rats. Therefore, it can be concluded that Anti-hyperglycemic property of Oyster mushroom could be explained through increased expression of AMPK and activation of CREB.Bangladesh Journal of Medical Science Vol.17(4) 2018 p.661-668

Oyster mushroom functions as an anti-hyperglycaemic through phosphorylation of AMPK and increased expression of GLUT4 in type 2 diabetic model rats

Objectives

Traditionally, mushrooms have been used to reduce hyperglycaemia. However, the mechanism underlying this effect has not yet been explored. AMP-activated protein kinase (AMPK) is known to reduce hyperglycaemia through an insulin-independent pathway. This study aimed to observe the effect of oyster mushroom powder (OMP) on phosphorylation of AMPK (p-AMPK) and expression of GLUT4 mRNA in diabetic model rats.

Methods

Long-Evans rats were used to develop type 2 diabetic model rats through intraperitoneal induction of streptozotocin (STZ). OMP was supplemented at 5% with the usual feed of rats for 8 consecutive weeks. Then, the rats were sacrificed. RNA was extracted by the TRIzol reagent, and proteins were extracted from different tissues with RIPA lysis buffer. Expression of GLUT4 mRNA was measured through cDNA-PCR techniques, and p-AMPK was detected using western blotting. The band intensities of the PCR products and proteins were measured using Image J software.

Results

Supplementation of OMP for 8 weeks resulted in a reduction of the serum glucose level in STZ-induced, type 2 diabetic model rats. The levels of p-AMPK, as a ratio relative to β-actin, increased in the muscle and adipose tissues of mushroom-treated type 2 diabetic model rats, compared to those in control diabetic model rats. Expression of GLUT4, as a ratio relative to GAPDH, increased significantly in both the muscle and adipose tissues of mushroom-treated diabetic rats.

Conclusion

Oyster mushroom may decrease hyperglycaemia through increased p-AMPK and also expression of GLUT4 in the muscle and adipose tissues.

Characterization of ammonia binding to the second coordination shell of the oxygen-evolving complex of photosystem II

The second-shell ammonia binding sites near the oxygen-evolving complex are characterized by Continuum Electrostatic/Monte Carlo (MCCE), QM/MM and DFT calculations and experimental measurements.

Localization and dynamics of the anticarcinogenic curcumin with GM1 and other miceller assemblies

Structural transitions involving shape changes play an important role in cellular physiology and enhance the bioavailability of the natural food like curcumin in surfactant aggregates. In this work, we have studied the localization, dynamics and stability of curcumin in various miceller assemblies using a combination of absorbance and fluorescence spectroscopic approaches. The measurements of absorption and fluorescence spectra of curcumin revealed that the nature of interactions of ionic and nonionic surfactants and the glycosphingolipid, GM₁ with curcumin is significantly different with surfactant concentrations. At low concentrations of SDS and the GM₁ the head group of SDS and GM₁ binds to the central β-diketone group of curcumin to form SDS-curcumin or GM₁-curcumin complexes. At high concentrations, both formed micelles with curcumin completely solubilized inside. Cucurmin is solubilized in the stern layer of SDS micelles. Compared to spherical micelles, rod shaped micelles allow more curcumin to bind through hydrophobic interactions indicated by higher absorption and fluorescence, enhanced partition coefficient and stability. Whereas curcumin associates with GM₁ micelles with lower partition coefficient, solubility and remain closer to aqueous phase decreasing its bioavailability and stability. While cucurmin is solubilized in the palisade layer of deoxycholate and octyl glucopyranoside micelles through the alkyl chains providing more hydrophobic microenvironment to curcumin with enhanced stability and bioavailability. Graphical abstract Schematic diagram of the two different types of detergent micelles and larger GM1 micelles.

BACTERIA ASSOCIATED WITH NON-ALCOHOLIC FERMENTED BAMBOO SHOOT FOOD PRODUCT

Pure bacterial cultures were isolated from fermented products collected from two locations of North East India (Assam and Arunachal Pradesh). Forty four variants were identified by 16S rRNA gene sequencing. The dominant microbial genera found were Bacillus, Paenibacillus followed by Oceanobacillus and Lactobacillus in Assam and Bacillus, Enterococcus, Lactobacillus in Arunachal-Pradesh food products. Bacillus isolates showed extracellular enzyme production (amylases, proteases and lipases) as analyzed through plate assay. GC-MS analysis showed beneficial chemical components like organic acids, esters, aminoacids, vitamins in fermented bamboo shoot products. Probiotic attributes of culturable bacterial isolates from bamboo fermentations gives promiscuity for human consumption. Beneficial microorganisms from bamboo shoot fermented food products of North-Eastern region of India were explored and compared using bioinformatics tools.