Complete genome sequence of carbapenem-resistant pathogenic Klebsiella aerogenes strain CH7 isolated from vermicompost

We announce the complete genome of Klebsiella aerogenes strain CH7, isolated from a vermicompost sample. A total of 9.14131 million high-quality reads comprised 96 contigs with 5,273 genes and 5,038 protein-coding genes.

Resolving the polycistronic aftermath: Essential role of topoisomerase IA in preventing R-loops in Leishmania

Kinetoplastid parasites are "living bridges" in the evolution from prokaryotes to higher eukaryotes. The near-intronless genome of the kinetoplastid Leishmania exhibits polycistronic transcription which can facilitate R-loop formation. Therefore, to prevent such DNA-RNA hybrids, Leishmania has retained prokaryotic-like DNA Topoisomerase IA (LdTOPIA) in the course of evolution. LdTOPIA is an essential enzyme that is expressed ubiquitously and is adapted for the compartmentalized eukaryotic form in harboring functional bipartite nuclear localization signals. Although exhibiting greater homology to mycobacterial TOPIA, LdTOPIA could functionally complement the growth lethality of Escherichia coli TOPIA null GyrB ts strain at non-permissive temperatures. Purified LdTOPIA exhibits Mg2+-dependent relaxation of only negatively supercoiled DNA and preference towards single-stranded DNA substrates. LdTOPIA prevents nuclear R-loops as conditional LdTOPIA downregulated parasites exhibit R-loop formation and thereby parasite killing. The clinically used tricyclic antidepressant, norclomipramine could specifically inhibit LdTOPIA and lead to R-loop formation and parasite elimination. This comprehensive study therefore paves an avenue for drug repurposing against Leishmania.

Understanding the basis of thermostability for enzyme "Nanoluc" towards designing industry-competent engineered variants

As a leading contender in the study of luminescence, nanoluciferase has recently attracted attention and proven effective in a wide variety of research areas. Although numerous attempts have been made to improve activity, there has yet to be a thorough exploration of further possibilities to improve thermostability. In this study, protein engineering in tandem with molecular dynamics simulation at various temperatures (300 K, 400 K, 450 K and 500 K) was used to improve our understanding of nanoluciferase dynamics and identification of factors that could significantly enhance the thermostability. Based on these, three novel mutations have been narrowed down, which were hypothesised to improve thermostability. Root mean square deviation and root mean square fluctuation studies confirmed higher stability of mutant at high temperature. Solvent-accessible surface area and protein unfolding studies revealed a decreased tendency of mutant to unfold at higher temperatures. Further free energy landscape and principal component analysis was adapted to get deeper insights into the thermodynamic and structural behavior of these proteins at elevated temperature. Thus, this study provides a deeper insight into the dynamic factors for thermostability and introduces a novel, enhanced nanoluciferase candidate with potential use in industry.Communicated by Ramaswamy H. Sarma.

Tests of Light-Lepton Universality in Angular Asymmetries of B^{0}→D^{*-}ℓν Decays

We present the first comprehensive tests of the universality of the light leptons in the angular distributions of semileptonic B^{0}-meson decays to charged spin-1 charmed mesons. We measure five angular-asymmetry observables as functions of the decay recoil that are sensitive to lepton-universality-violating contributions. We use events where one neutral B is fully reconstructed in ϒ(4S)→BB[over ¯] decays in data corresponding to 189  fb^{-1} integrated luminosity from electron-positron collisions collected with the Belle II detector. We find no significant deviation from the standard model expectations.

Precise Measurement of the D_{s}^{+} Lifetime at Belle II

We measure the lifetime of the D_{s}^{+} meson using a data sample of 207  fb^{-1} collected by the Belle II experiment running at the SuperKEKB asymmetric-energy e^{+}e^{-} collider. The lifetime is determined by fitting the decay-time distribution of a sample of 116×10^{3} D_{s}^{+}→ϕπ^{+} decays. Our result is τ_{D_{s}^{+}}=(499.5±1.7±0.9)  fs, where the first uncertainty is statistical and the second is systematic. This result is significantly more precise than previous measurements.

Search for a τ^{+}τ^{-} Resonance in e^{+}e^{-}→μ^{+}μ^{-}τ^{+}τ^{-} Events with the Belle II Experiment

We report the first search for a nonstandard-model resonance decaying into τ pairs in e^{+}e^{-}→μ^{+}μ^{-}τ^{+}τ^{-} events in the 3.6-10  GeV/c^{2} mass range. We use a 62.8  fb^{-1} sample of e^{+}e^{-} collisions collected at a center-of-mass energy of 10.58 GeV by the Belle II experiment at the SuperKEKB collider. The analysis probes three different models predicting a spin-1 particle coupling only to the heavier lepton families, a Higgs-like spin-0 particle that couples preferentially to charged leptons (leptophilic scalar), and an axionlike particle, respectively. We observe no evidence for a signal and set exclusion limits at 90% confidence level on the product of cross section and branching fraction into τ pairs, ranging from 0.7 to 24 fb, and on the couplings of these processes. We obtain world-leading constraints on the couplings for the leptophilic scalar model for masses above 6.5  GeV/c^{2} and for the axionlike particle model over the entire mass range.

Measurement of CP Violation in B^{0}→K_{S}^{0}π^{0} Decays at Belle II

We report a measurement of the CP-violating parameters C and S in B^{0}→K_{S}^{0}π^{0} decays at Belle II using a sample of 387×10^{6}  BB[over ¯] events recorded in e^{+}e^{-} collisions at a center-of-mass energy corresponding to the ϒ(4S) resonance. These parameters are determined by fitting the proper decay-time distribution of a sample of 415 signal events. We obtain C=-0.04_{-0.15}^{+0.14}±0.05 and S=0.75_{-0.23}^{+0.20}±0.04, where the first uncertainties are statistical and the second are systematic.

Test of Light-Lepton Universality in the Rates of Inclusive Semileptonic B-Meson Decays at Belle II

We present the first measurement of the ratio of branching fractions of inclusive semileptonic B-meson decays, R(X_{e/μ})=B(B→Xeν)/B(B→Xμν), a precision test of electron-muon universality, using data corresponding to 189  fb^{-1} from electron-positron collisions collected with the Belle II detector. In events where the partner B meson is fully reconstructed, we use fits to the lepton momentum spectra above 1.3  GeV/c to obtain R(X_{e/μ})=1.007±0.009(stat)±0.019(syst), which is the most precise lepton-universality test of its kind and agrees with the standard-model expectation.

An insight into omics analysis and metabolic pathway engineering of lignin-degrading enzymes for enhanced lignin valorization

Lignin, a highly heterogeneous polymer of lignocellulosic biomass, is intricately associated with cellulose and hemicellulose, responsible for its strength and rigidity. Lignin decomposition is carried out through certain enzymes derived from microorganisms to promote the hydrolysis of lignin. Analyzing multi-omics data helps to emphasize the probable value of fungal-produced enzymes to degrade the lignocellulosic material, which provides them an advantage in their ecological niches. This review focuses on lignin biodegrading microorganisms and associated ligninolytic enzymes, including lignin peroxidase, manganese peroxidase, versatile peroxidase, laccase, and dye-decolorizing peroxidase. Further, enzymatic catalysis, lignin biodegradation mechanisms, vital factors responsible for lignin modification and degradation, and the design and selection of practical metabolic pathways are also discussed. Highlights were made on metabolic pathway engineering, different aspects of omics analyses, and its scope and applications to ligninase enzymes. Finally, the advantages and essential steps of successfully applying metabolic engineering and its path forward have been addressed.

Loss of PI3Kα Mediates Protection From Myocardial Ischemia-Reperfusion Injury Linked to Preserved Mitochondrial Function

Background Identifying new therapeutic targets for preventing the myocardial ischemia-reperfusion injury would have profound implications in cardiovascular medicine. Myocardial ischemia-reperfusion injury remains a major clinical burden in patients with coronary artery disease. Methods and Results We studied several key mechanistic pathways known to mediate cardioprotection in myocardial ischemia-reperfusion in 2 independent genetic models with reduced cardiac phosphoinositide 3-kinase-α (PI3Kα) activity. P3Kα-deficient genetic models (PI3KαDN and PI3Kα-Mer-Cre-Mer) showed profound resistance to myocardial ischemia-reperfusion injury. In an ex vivo reperfusion protocol, PI3Kα-deficient hearts had an 80% recovery of function compared with ≈10% recovery in the wild-type. Using an in vivo reperfusion protocol, PI3Kα-deficient hearts showed a 40% reduction in infarct size compared with wild-type hearts. Lack of PI3Kα increased late Na⁺ current, generating an influx of Na⁺, facilitating the lowering of mitochondrial Ca²⁺, thereby maintaining mitochondrial membrane potential and oxidative phosphorylation. Consistent with these functional differences, mitochondrial structure in PI3Kα-deficient hearts was preserved following ischemia-reperfusion injury. Computer modeling predicted that PIP3, the product of PI3Kα action, can interact with the murine and human Na_V1.5 channels binding to the hydrophobic pocket below the selectivity filter and occluding the channel. Conclusions Loss of PI3Kα protects from global ischemic-reperfusion injury linked to improved mitochondrial structure and function associated with increased late Na⁺ current. Our results strongly support enhancement of mitochondrial function as a therapeutic strategy to minimize ischemia-reperfusion injury.

Search for an Invisible Z^{'} in a Final State with Two Muons and Missing Energy at Belle II

The L_{μ}-L_{τ} extension of the standard model predicts the existence of a lepton-flavor-universality-violating Z^{'} boson that couples only to the heavier lepton families. We search for such a Z^{'} through its invisible decay in the process e^{+}e^{-}→μ^{+}μ^{-}Z^{'}. We use a sample of electron-positron collisions at a center-of-mass energy of 10.58 GeV collected by the Belle II experiment in 2019-2020, corresponding to an integrated luminosity of 79.7  fb^{-1}. We find no excess over the expected standard-model background. We set 90%-confidence-level upper limits on the cross section for this process as well as on the coupling of the model, which ranges from 3×10^{-3} at low Z^{'} masses to 1 at Z^{'} masses of 8  GeV/c^{2}.

Search for Lepton-Flavor-Violating τ Decays to a Lepton and an Invisible Boson at Belle II

We search for lepton-flavor-violating τ^{-}→e^{-}α and τ^{-}→μ^{-}α decays, where α is an invisible spin-0 boson. The search uses electron-positron collisions at 10.58 GeV center-of-mass energy with an integrated luminosity of 62.8  fb^{-1}, produced by the SuperKEKB collider and collected with the Belle II detector. We search for an excess in the lepton-energy spectrum of the known τ^{-}→e^{-}ν[over ¯]_{e}ν_{τ} and τ^{-}→μ^{-}ν[over ¯]_{μ}ν_{τ} decays. We report 95% confidence-level upper limits on the branching-fraction ratio B(τ^{-}→e^{-}α)/B(τ^{-}→e^{-}ν[over ¯]_{e}ν_{τ}) in the range (1.1-9.7)×10^{-3} and on B(τ^{-}→μ^{-}α)/B(τ^{-}→μ^{-}ν[over ¯]_{μ}ν_{τ}) in the range (0.7-12.2)×10^{-3} for α masses between 0 and 1.6  GeV/c^{2}. These results provide the most stringent bounds on invisible boson production from τ decays.

Characterization of a Class A β-Lactamase from Francisella tularensis (Ftu-1) Belonging to a Unique Subclass toward Understanding AMR

β-lactamase production with vast catalytic divergence in the pathogenic strain limits the antibiotic spectrum in the clinical environment. Class A carbapenemase shares significant sequence similarities, structural features, and common catalytic mechanisms although their resistance spectrum differs from class A β-lactamase in carbapenem and monobactam hydrolysis. In other words, it limited the antibiotic treatment option against infection, causing carbapenemase-producing superbugs. Ftu-1 is a class A β-lactamase expressed by the Francisella tularensis strain, a potent causative organism of tularemia. The chromosomally encoded class A β-lactamase shares two conserved cysteine residues, a common characteristic of a carbapenemase, and a distinctive class in the phylogenetic tree. Complete biochemical and biophysical characterization of the enzyme was performed to understand the overall stability and environmental requirements to perform optimally. To comprehend the enzyme-drug interaction and its profile toward various chemistries of β-lactam and β-lactamase inhibitors, comprehensive kinetic and thermodynamic analyses were conducted using various β-lactam drugs. The dynamic property of Ftu-1 β-lactamase was also predicted using molecular dynamics (MD) simulation to compare its loop flexibility and ligand binding with other related class A β-lactamases. Overall, this study fosters a comprehensive understanding of Ftu-1, proposed to be an intermediate class by characterizing its kinetic profiling, stability by biochemical and biophysical methodologies, and susceptibility profiling. This understanding would be beneficial for the design of new-generation therapeutics.

Observation of e^{+}e^{-}→ωχ_{bJ}(1P) and Search for X_{b}→ωϒ(1S) at sqrt[s] near 10.75 GeV

We study the processes e^{+}e^{-}→ωχ_{bJ}(1P) (J=0, 1, or 2) using samples at center-of-mass energies sqrt[s]=10.701, 10.745, and 10.805 GeV, corresponding to 1.6, 9.8, and 4.7  fb^{-1} of integrated luminosity, respectively. These data were collected with the Belle II detector during special operations of the SuperKEKB collider above the ϒ(4S) resonance. We report the first observation of ωχ_{bJ}(1P) signals at sqrt[s]=10.745  GeV. By combining Belle II data with Belle results at sqrt[s]=10.867  GeV, we find energy dependencies of the Born cross sections for e^{+}e^{-}→ωχ_{b1,b2}(1P) to be consistent with the shape of the ϒ(10753) state. These data indicate that the internal structures of the ϒ(10753) and ϒ(10860) states may differ. Including data at sqrt[s]=10.653  GeV, we also search for the bottomonium equivalent of the X(3872) state decaying into ωϒ(1S). No significant signal is observed for masses between 10.45 and 10.65  GeV/c^{2}.

Measurement of the Λ_{c}^{+} Lifetime

An absolute measurement of the Λ_{c}^{+} lifetime is reported using Λ_{c}^{+}→pK^{-}π^{+} decays in events reconstructed from data collected by the Belle II experiment at the SuperKEKB asymmetric-energy electron-positron collider. The total integrated luminosity of the data sample, which was collected at center-of-mass energies at or near the ϒ(4S) resonance, is 207.2  fb^{-1}. The result, τ(Λ_{c}^{+})=203.20±0.89±0.77  fs, where the first uncertainty is statistical and the second systematic, is the most precise measurement to date and is consistent with previous determinations.

Search for a Dark Photon and an Invisible Dark Higgs Boson in μ^{+}μ^{-} and Missing Energy Final States with the Belle II Experiment

The dark photon A^{'} and the dark Higgs boson h^{'} are hypothetical particles predicted in many dark sector models. We search for the simultaneous production of A^{'} and h^{'} in the dark Higgsstrahlung process e^{+}e^{-}→A^{'}h^{'} with A^{'}→μ^{+}μ^{-} and h^{'} invisible in electron-positron collisions at a center-of-mass energy of 10.58 GeV in data collected by the Belle II experiment in 2019. With an integrated luminosity of 8.34  fb^{-1}, we observe no evidence for signal. We obtain exclusion limits at 90% Bayesian credibility in the range of 1.7-5.0 fb on the cross section and in the range of 1.7×10^{-8}-200×10^{-8} on the effective coupling ϵ^{2}×α_{D} for the A^{'} mass in the range of 4.0  GeV/c^{2}<M_{A^{'}}<9.7  GeV/c^{2} and for the h^{'} mass M_{h^{'}}<M_{A^{'}}, where ϵ is the mixing strength between the standard model and the dark photon and α_{D} is the coupling of the dark photon to the dark Higgs boson. Our limits are the first in this mass range.

In silico modeling revealed new insights into the mechanism of action of enzyme 2'-5'-oligoadenylate synthetase in cattle

The innate immune system has an important role in developing the initial resistance to virus infection, and the ability of oligoadenylate synthetase to overcome viral evasion and enhance innate immunity is already established in humans. In the present study, we have tried to explore the molecular and structural variations present in Sahiwal (indigenous) and crossbred (Frieswal) cattle to identify the molecular mechanism of action of OAS1 gene in activation of innate immune response. The significant changes in structural alignment in terms of orientation of loops, shortening of β-sheets and formation of 3-10 α-helix was noticed in Sahiwal and Frieswal cattle. Further, it has been observed that OAS1 from Sahiwal had better binding with APC and DTP ligand than Frieswal OAS1. A remarkable change was seen in orientation at the nucleoside base region of both the ligands, which are bound with OAS1 protein from Frieswal and Sahiwal cattle. The Molecular Dynamic study of apo and ligand complex structures was provided more insight towards the stability of OAS1 from both cattle. This analysis displayed that the Sahiwal cattle protein has more steady nature throughout the simulation and has better binding towards Frieswal in terms of APC and DTP binding. Thus, OAS1 protein is the potential target for explaining the innate immune response in Sahiwal than Frieswal.Communicated by Ramaswamy H. Sarma.

P-324 Effectiveness of letrozole in symptomatic women with adenomyosis undergoing IVF: An overview of clinical features, sonographic characteristics, and reproductive outcome

Study question

Is letrozole pre-treatment a cost-effective option in improving symptoms, sonographic features, and reproductive outcomes in women with adenomyosis, undergoing IVF treatment?

Summary answer

Only two months of low dose letrozole pre-treatment is as effective as GnRH-agonist in symptomatic adenomyosis while significantly reducing the cost of treatment.

What is known already

About 20%–25% of women undergoing IVF present with adenomyosis and many of them suffer from dysmenorrhea and menorrhagia. Adenomyosis is often underdiagnosed and neglected uterine pathology which has a major bearing on the quality of life and fertility. Since adenomyosis is an estrogen-dependent disorder, letrozole, an aromatase inhibitor (controls estrogen production) is reported to be effective in improving symptoms of adenomyosis similar to GnRH-agonist but its role as before treatment IVF is unclear. Although GnRH-agonist is an established and effective pre-treatment option, is expensive and comes with the concerns like menopausal symptoms, increased gonadotropin doses, and duration of stimulation.

Study design, size, duration

This longitudinal, randomized cohort study was conducted at a tertiary-care hospital during June-2019 and November-2021. 194 adenomyosis women with symptoms undergoing fresh-cycle IVF, were screened and 147 recruited. These women were resistant to OCPs/progestins for symptomatic relief. 72 patients were treated with letrozole and 75 with GnRH-agonist for 2 months, and changes in their sonographic features and symptoms were evaluated before and after treatment. Reproductive outcomes were also compared between the treatment groups after IVF.

Participants/materials, setting, methods

Adenomyosis was diagnosed on 2D-TVS according to MUSA criteria. Among them, 72 patients were treated with 2.5 mg letrozole (only thrice weekly instead of conventional 2.5mg/daily) and 75 women were treated with GnRH-agonist depot (3.6mg/month) for 2 months. Patients were evaluated before and after 2 months of treatment for improvements in dysmenorrhea (VAS score) and menorrhagia (PBAC score), and quantitative scoring of sonographic features. Reproductive outcomes were also compared after both treatment.

Main results and the role of chance

The majority of women had 3-4 sonographic criteria on TVS (median of 3), such as irregular or interrupted junctional zone (79.49%), asymmetrical thickening of the myometrium (71.15%), globular uterus (43.59%), and myometrial cyst (33.33%). Significant reductions in the sonographic severity scores for diffuse adenomyosis, adenomyoma, and asymmetry in myometrial thickness were observed following both the treatment (p &lt; 0.05). The effects of both the treatments were comparable in terms of severity of sonographic features (p &gt; 0.05). Significant decreases in dysmenorrhea (letrozole: pre-7.76±1.6, post-1.74±0.58; GnRH-agonist: pre-7.92±2.1, post-0) and menorrhagia (letrozole: pre-169±31, post-73±18; GnRH-agonist: pre-171±25, post-12±6) were observed after 2 months in both the treatment (p &lt; 0.05). Since GnRH-agonist treated women experienced cessation of menstruation, the VAS and PBAC scores were not directly comparable between the groups after treatment. All fresh cycle IVF women were included to understand the effect of pre-treatment of these women. Following fresh cycle IVF, clinical pregnancy (23.61%, 25.33%), miscarriage rate (35.29%, 36.84%), and live birth rate (12.5%, 13.33%), respectively for letrozole and GnRH-agonist groups were comparable (p &gt; 0.05). The cost of the treatment was 19 times less with letrozole pre-treatment when compared with GnRH-agonist, while a comparable reduction in symptoms and IVF outcome parameters were observed.

Limitations, reasons for caution

A possible limitation is the lack of a proper blinding due to different routes of administration of the therapies. In the absence of a standardized classification of severity, we have used the TVS based scoring proposed by Lazzeri et al (2018), which is not universally accepted or independently validated.

Wider implications of the findings

Low-dose letrozole pre-treatment for 2 months is an attractive option before IVF for symptoms relief and comparable reproductive outcome to that of GnRH-agonist but with lower cost and without over-suppression of pituitary. This protocol may also be extended to women in general who are suffering from symptomatic adenomyosis.

Trial registration number

CTRI/2019/01/016919 [04/01/2019]

Synthesis of Dihydrobenzofuro[3,2-b]chromenes as a potential 3CLpro inhibitors of SARS-CoV-2: A molecular docking and dynamics simulation study

The recent emergence of pandemic of coronavirus (COVID‐19) caused by SARS‐CoV‐2 has raised significant global health concerns. More importantly, there is no specific therapeutics currently available to combat against this deadly infection. The enzyme 3‐chymotrypsin‐like cysteine protease (3CLpro) is known to be essential for viral life cycle as it controls the coronavirus replication. 3CLpro could be a potential drug target as established before in the case of severe acute respiratory syndrome coronavirus (SARS‐CoV) and Middle East respiratory syndrome coronavirus (MERS‐CoV). In the current study, we wanted to explore the potential of fused flavonoids as 3CLpro inhibitors. Fused flavonoids (5a,10a‐dihydro‐11H‐benzofuro[3,2‐b]chromene) are unexplored for their potential bioactivities due to their low natural occurrences. Their synthetic congeners are also rare due to unavailability of general synthetic methodology. Here we designed a simple strategy to synthesize 5a,10a‐dihydro‐11H‐benzofuro[3,2‐b]chromene skeleton and it's four novel derivatives. Our structural bioinformatics study clearly shows excellent potential of the synthesized compounds in comparison to experimentally validated inhibitor N3. Moreover, in‐silico ADMET study displays excellent druggability and extremely low level of toxicity of the synthesized molecules. Further, for better understanding, the molecular dynamic approach was implemented to study the change in dynamicity after the compounds bind to the protein. A detailed investigation through clustering analysis and distance calculation gave us sound comprehensive data about their molecular interaction. In summary, we anticipate that the currently synthesized molecules could not only be a potential set of inhibitors against 3CLpro but also the insights acquired from the current study would be instrumental in further developing novel natural flavonoid based anti‐COVID therapeutic spectrums.

Anti-hypertensive Peptide Predictor: A Machine Learning-Empowered Web Server for Prediction of Food-Derived Peptides with Potential Angiotensin-Converting Enzyme-I Inhibitory Activity

Angiotensin converting enzyme-I (ACE-I) is a key therapeutic target of the renin-angiotensin-aldosterone system (RAAS), the central pathway of blood pressure regulation. Food-derived peptides with ACE-I inhibitory activities are receiving significant research attention. However, identification of ACE-I inhibitory peptides from different food proteins is a labor-intensive, lengthy, and expensive process. For successful identification of potential ACE-I inhibitory peptides from food sources, a machine learning and structural bioinformatics-based web server has been developed and reported in this study. The web server can take input in the FASTA format or through UniProt ID to perform the in silico gastrointestinal digestion and then screen the resulting peptides for ACE-I inhibitory activity. This unique platform provides elaborated structural and functional features of the active peptides and their interaction with ACE-I. Thus, it can potentially enhance the efficacy and reduce the time and cost in identifying and characterizing novel ACE-I inhibitory peptides from food proteins. URL: http://hazralab.iitr.ac.in/ahpp/index.php.

Precise Measurement of the D^{0} and D^{+} Lifetimes at Belle II

We report a measurement of the D^{0} and D^{+} lifetimes using D^{0}→K^{-}π^{+} and D^{+}→K^{-}π^{+}π^{+} decays reconstructed in e^{+}e^{-}→cc[over ¯] data recorded by the Belle II experiment at the SuperKEKB asymmetric-energy e^{+}e^{-} collider. The data, collected at center-of-mass energies at or near the ϒ(4S) resonance, correspond to an integrated luminosity of 72  fb^{-1}. The results, τ(D^{0})=410.5±1.1(stat)±0.8(syst)  fs and τ(D^{+})=1030.4±4.7(stat)±3.1(syst)  fs, are the most precise to date and are consistent with previous determinations.

Search for B^{+}→K^{+}νν[over ¯] Decays Using an Inclusive Tagging Method at Belle II

A search for the flavor-changing neutral-current decay B^{+}→K^{+}νν[over ¯] is performed at the Belle II experiment at the SuperKEKB asymmetric energy electron-positron collider. The data sample corresponds to an integrated luminosity of 63  fb^{-1} collected at the ϒ(4S) resonance and a sample of 9  fb^{-1} collected at an energy 60 MeV below the resonance. Because the measurable decay signature involves only a single charged kaon, a novel measurement approach is used that exploits not only the properties of the B^{+}→K^{+}νν[over ¯] decay, but also the inclusive properties of the other B meson in the ϒ(4S)→BB[over ¯] event, to suppress the background from other B meson decays and light-quark pair production. This inclusive tagging approach offers a higher signal efficiency compared to previous searches. No significant signal is observed. An upper limit on the branching fraction of B^{+}→K^{+}νν[over ¯] of 4.1×10^{-5} is set at the 90% confidence level.

Variations in the SDN Loop of Class A Beta-Lactamases: A Study of the Molecular Mechanism of BlaC (Mycobacterium tuberculosis) to Alter the Stability and Catalytic Activity Towards Antibiotic Resistance of MBIs

The emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis calls for an immediate search for novel treatment strategies. Recently, BlaC, the principal beta-lactamase of Mycobacterium tuberculosis, was recognized as a potential therapeutic target. BlaC belongs to Ambler class A, which is generally susceptible to the beta-lactamase inhibitors currently used in clinics: tazobactam, sulbactam, and clavulanate. Alterations at Ser130 in conserved SDN loop confer resistance to mechanism-based inhibitors (MBIs) commonly observed in various clinical isolates. The absence of clinical evidence of S130G conversion in M. tuberculosis draws our attention to build laboratory mutants of S130G and S130A of BlaC. The study involving steady state, inhibition kinetics, and fluorescence microscopy shows the emergence of resistance against MBIs to the mutants expressing S130G and S130A. To understand the molecular reasoning behind the unavailability of such mutation in real life, we have used circular dichroism (CD) spectroscopy, differential scanning calorimetry (DSC), molecular dynamics (MD) simulation, and stability-based enzyme activity to compare the stability and dynamic behaviors of native and S130G/A mutant form of BlaC. A significant decrease in melting temperature (BlaC T_M 60°C, S130A T_M 50°C, and S130G T_M 45°C), kinetic instability at higher temperature, and comparative dynamic instability correlate the fact that resistance to beta-lactam/beta-lactamase inhibitor combinations will likely not arise from the structural alteration of BlaC, therefore establishing confidence that this therapeutic modality can be potentially applied as a part of a successful treatment regimen against M. tuberculosis.

Immunogenicity and safety of two monovalent rotavirus vaccines, ROTAVAC® and ROTAVAC 5D® in Zambian infants

BACKGROUND AND AIMS

ROTAVAC® (frozen formulation stored at -20 °C) and ROTAVAC 5D® (liquid formulation stable at 2-8 °C) are rotavirus vaccines derived from the 116E human neonatal rotavirus strain, developed and licensed in India. This study evaluated and compared the safety and immunogenicity of these vaccines in an infant population in Zambia.

METHODS

We conducted a phase 2b, open-label, randomized, controlled trial wherein 450 infants 6 to 8 weeks of age were randomized equally to receive three doses of ROTAVAC or ROTAVAC 5D, or two doses of ROTARIX®. Study vaccines were administered concomitantly with routine immunizations. Blood samples were collected pre-vaccination and 28 days after the last dose. Serum anti-rotavirus IgA antibodies were measured by ELISA, with WC3 and 89-12 rotavirus strains as viral lysates in the assays. The primary analysis was to assess non-inferiority of ROTAVAC 5D to ROTAVAC in terms of the geometric mean concentration (GMC) of serum IgA (WC3) antibodies. Seroresponse and seropositivity were also determined. Safety was evaluated as occurrence of immediate, solicited, unsolicited, and serious adverse events after each dose.

RESULTS

The study evaluated 388 infants in the per-protocol population. All three vaccines were well tolerated and immunogenic. The post-vaccination GMCs were 14.0 U/mL (95% CI: 10.4, 18.8) and 18.1 U/mL (95% CI: 13.7, 24.0) for the ROTAVAC and ROTAVAC 5D groups, respectively, yielding a ratio of 1.3 (95% CI: 0.9, 1.9), thus meeting the pre-set non-inferiority criteria. Solicited and unsolicited adverse events were similar across all study arms. No death or intussusception case was reported during study period.

CONCLUSIONS

Among Zambian infants, both ROTAVAC and ROTAVAC 5D were well tolerated and the immunogenicity of ROTAVAC 5D was non-inferior to that of ROTAVAC. These results are consistent with those observed in licensure trials in India and support use of these vaccines across wider geographical areas.

A comprehensive characterization of novel CYP-BM3 homolog (CYP-BA) from Bacillus aryabhattai

Functionalizing C-H bond poses one of the most significant challenges for chemists providing them with very few substrate-specific synthetic routes. Despite being incredibly plastic in their enzymatic ability, they are confined with deficient enzymatic action and limited explicitness of the substrates. In this study, we have endeavored to characterize novel cytochrome P450 from Bacillus aryabhattai (CYP-BA), a homolog of CYP P450-BM3, by taking interdisciplinary approaches. We conducted structure and sequence comparison to understand the conservation pattern for active site residues, conserved fold, evolutionary relationships among others. Molecular dynamics simulations were performed to understand the dynamic nature and interaction with the substrates. CYP-BA was successfully cloned, purified, and characterized. The enzyme's stability toward various physicochemical parameters was evaluated by UV-vis spectroscopy and Circular Dichroism (CD) spectroscopy. Various saturated fatty acids being the natural cytochrome P450 substrates were evaluated as catalytic efficiency of substrate oxidation by CYP-BA. The binding affinity of these natural substrates was monitored against CYP-BA by isothermal titration calorimetry (ITC). The catalytic performance of CYP-BA was satisfactory enough to proceed to the next step, that is, engineering to expand the substrate range to include polycyclic aromatic hydrocarbons (PAH). This is the first evidence of cloning, purifying and characterizing a novel homolog of CYP-BM3 to enable a better understanding of this novel biocatalyst and to provide a platform toward expanding its catalytic process through enzyme engineering.

Vitreous substitutes: An overview of the properties, importance, and development

Vitreous or vitreous humor is a complex transparent gel that fills the space between the lens and retina of an eye and acts as a transparent medium that allows light to pass through it to reach the photoreceptor layer (retina) of the eye. The vitreous humor is removed in ocular surgery (vitrectomy) for pathologies like retinal detachment, macular hole, diabetes-related vitreous hemorrhage detachment, and ocular trauma. Since the vitreous is not actively regenerated or replenished, there is a need for a vitreous substitute to fill the vitreous cavity to provide a temporary or permanent tamponade to the retina following some vitreoretinal surgeries. An ideal vitreous substitute could probably be left inside the eye forever. The vitreous humor is transparent, biocompatible, viscoelastic and highly hydrophilic; polymeric hydrogels with these properties can be a potential candidate to be used as vitreous substitutes. To meet the tremendous demand for the vitreous substitute, many scientists all over the world have developed various kinds of vitreous substitutes or tamponade agent. Vitreous substitutes, whatsoever developed till date, are associated with several advantages and disadvantages, and there is no ideal vitreous substitute available till date. This review highlights the polymer-based vitreous substitutes developed so far, along with their advantages and limitations. The gas-based and oil-based substitutes have also been discussed but very briefly.

N-terminal truncation of VC0395_0300 protein from Vibrio cholerae does not lead to loss of diguanylate cyclase activity

The bacterial secondary messenger bis-(3',5')-cyclic-dimeric-guanosine monophosphate (c-di-GMP) has been implicated in the pathogenesis of Vibrio cholerae, due to its significant role in regulating the virulence, biofilm formation and motility of the host organism. The VC0395_0300 protein from V. cholerae, possessing a GGEEF sequence has been established as a diguanylate cyclase (DGC) capable of catalyzing the conversion of two GTP molecules to form cyclic-di-GMP. This in turn, plays a crucial role in allowing the organism to adopt a dual lifestyle, thriving both in human and aquatic systems. The difficulty in procuring sufficient amounts of homogenous soluble protein for structural assessment of the GGDEF domain in VC0395_0300 and the lack of soluble protein yield, prompted the truncation into smaller constructs (Sebox31 and Sebox32) carrying the GGDEF domain. The truncates retained their diguanylate cyclase activity comparable to the wild type, and were able to form biofilms as well. Fluorescence and circular dichroism spectroscopy measurements revealed that the basic structural elements do not show significant changes in the truncated proteins as compared to the full-length. This has also been confirmed using homology modeling and molecular docking of the wild type and truncates. This led us to conclude that the truncated constructs retain their activity in spite of the deletions in the N terminal region. This is supportive of the fact that DGC activity in GGDEF proteins is predominantly dependent on the presence of the conserved GGD(/E)EF domain and its interaction with GTP.

Characterization of a putative ribosome binding site at the 5' untranslated region of bovine heat shock protein 90

Untranslated regions (UTRs) of the transcripts play significant roles in translation regulation and continue to raise many intriguing questions in our understanding of cellular stress physiology. Internal ribosome entry site (IRES) mediated alternative translation initiations are emerging as unique mechanisms. Present study is aimed to indentify a functional short 92 base pair length putative sequence located at the 5' untranslated region of bovine heat shock protein 90 AA1 (Hsp90AA1) may interact with ribosomal as well as eukaryotic initiation factor binding site. Here we have predicted both the two and three dimensional structures of bovine Hsp90AA1 IRES (MF400854) element with their respective free energy. Molecular interactions between bovine RPS5 and IRES have been determined after the preparation of docking complex of IRES bound RPS5. Structure of bovine ribosomal translational initiation factor (TIF) has also been determined and docked with IRES. Molecular interaction between bovine TIF and IRES was analyzed from the complex structure. We further detected the relative expression efficiency of the viral (original) in relation with Hsp90AA1 IRES-driven GFP expression, which revealed that efficiency under the control of identified bovine Hsp90AA1 IRES was slightly lower than viral origin. It was also noted that identified bovine HSP90 IRES may increase the expression level of GFP under in vitro heat stressed condition.

Ribosylation induced structural changes in Bovine Serum Albumin: understanding high dietary sugar induced protein aggregation and amyloid formation

Non-enzymatic glycation of proteins is believed to be the root cause of high dietary sugar associated pathophysiological maladies. We investigated the structural changes in protein during progression of glycation using ribosylated Bovine Serum Albumin (BSA). Non enzymatic attachment of about 45 ribose molecules to BSA resulted in gradual reduction of hydrophobicity and aggregation as indicated by red-shifted tryptophan fluorescence, reduced ANS binding and lower anisotropy of FITC-conjugated protein. Parallely, there was a significant decrease of alpha helicity as revealed by Circular Dichroism (CD) and Fourier transformed-Infra Red (FT-IR) spectra. The glycated proteins assumed compact globular structures with enhanced Thioflavin-T binding resembling amyloids. The gross structural transition affected by ribosylation led to enhanced thermostability as indicated by melting temperature and Transmission Electron Microscopy. At a later stage of glycation, the glycated proteins developed non-specific aggregates with increase in size and loss of amyloidogenic behaviour. A parallel non-glycated control incubated under similar conditions indicated that amyloid formation and associated changes were specific for ribosylation and not driven by thermal denaturation due to incubation at 37 °C. Functionality of the glycated protein was significantly altered as probed by Isothermal Titration Calorimetry using polyphenols as substrates. The studies demonstrated that glycation driven globular amyloids form and persist as transient intermediates during formation of misfolded glycated adducts. To the best of our knowledge, the present study is the first systematic attempt to understand glycation associated changes in a protein and provides important insights towards designing therapeutics for arresting dietary sugar induced amyloid formation.

Effect of utilization of crude glycerol as substrate on fatty acid composition of an oleaginous yeast Rhodotorula mucilagenosa IIPL32: Assessment of nutritional indices

This work studied the use of crude glycerol obtained from biodiesel industry as substrate to generate yeast lipid from Rhodotorula mucilagenosa IIPL32 MTCC 25056. Crude glycerol is a low value by product obtained from biodiesel industry. Rhodotorula mucilagenosa IIPL32 MTCC 25056 was evaluated for its potential to produce lipid using crude glycerol as sole source of carbon. Under nitrogen limiting condition a lipid and biomass content of 5.6 g/L and19.7 g/L were obtained from crude glycerol. The fatty acid profile was found to be interestingly rich in oleic acid (61.88%), linoleic acid (16.17%) and linolenic acid (1.03%) comprising ~80% of MUFA and PUFA of total lipid. Further, evaluations were attempted to compare MUFA rich yeast lipid against different plant-borne edible oils commonly used in India. In this study, nutritional indices were calculated to check feasibility of using yeast oil as a plausible blend to edible oil.

Scale-up strategy for yeast single cell oil production for Rhodotorula mucilagenosa IIPL32 from corn cob derived pentosan

This work was aimed to strategically scale-up the yeast lipid production process using Reynolds number as a standard rheological parameter from 50 mL to 50 L scale. Oleaginous yeast Rhodotorula mucilaginosa IIPL32 was cultivated in xylose rich corncob hydrolysate. The fermentation process for growth and maturation was operated in fed-batch with two different C/N ratios of 40 and 60. The hydrodynamic parameters were used to standardize and represent the effect of rheology on the fermentation process. The growth pattern of the yeast was found similar in both shake flask and fermenter with the maximum growth observed at 48 h. The lipid yield increased from 0.4 g/L and 0.5 g/L to 1.3 g/L and 1.83 g/L for 50 mL to 50 L for C/N ratio 40 and 60 respectively. The increase in productivity during the growth phase and lipid accumulation during the maturation phase showed that the scale-up strategy was successful.

Understanding structure-based dynamic interactions of antihypertensive peptides extracted from food sources

Functional foods are emerging as essential healthy nutritional component due to their abundant wellbeing benefits. Especially the food-derived peptides are considered as key components for playing their biologically active roles. One such robust therapeutics that already exploited with food peptides that help treating high blood pressure via targeting Angiotensin-Converting Enzyme (ACE). This in silico study demonstrated the inhibitory potential of antihypertensive peptides derived from food sources. This study involves an intensive structure-based analysis of enzyme-peptide interactions using Molecular Dynamics (MD) simulations. Interestingly, this study will help us to get deeper understanding on how food peptides achieve successful inhibition of ACE. In this study, the peptide-enzyme complexes revealed two binding pockets, A and B, on either side of the active site Zn atom. Pocket B has a smaller binding site volume than pocket A, comprised of β-sheets and the active site opening cleft. The interface of the binding sites showed that the enzyme structure was negative to neutral charge, and the peptide structure was positive to neutral charge. The dynamics of complex structures of seven highly potential peptides were performed for 20 ns each at 300 K. Comparative analysis of RMSD, RMSF and binding energies show the enzyme-peptide complexes and the overall stability of apo-enzyme. Importantly, two peptides AFKAWAVAR and IWHHTF showed the highest variation in their RMSD as compared to the apo-enzyme. This study will further be useful for the assessment of the characteristics to predict novel inhibitory peptides that can be generated from food proteins.Communicated by Ramaswamy H. Sarma.

The basics of epithelial-mesenchymal transition (EMT): A study from a structure, dynamics, and functional perspective

Epithelial-mesenchymal transition (EMT) is a key step in transdifferentiation process in solid cancer development. Forthcoming evidence suggest that the stratified program transforms polarized, immotile epithelial cells to migratory mesenchymal cells associated with enhancement of breast cancer stemness, metastasis, and drug resistance. It involves primarily several signaling pathways, such as transforming growth factor-β (TGF-β), cadherin, notch, plasminogen activator protein inhibitor, urokinase plasminogen activator, and WNT/beta catenin pathways. However, current understanding on the crosstalk of multisignaling pathways and assemblies of key transcription factors remain to be explored. In this review, we focus on the crosstalk of signal transduction pathways linked to the current therapeutic and drug development strategies. We have also performed the computational modeling on indepth the structure and conformational dynamic studies of regulatory proteins and analyze molecular interactions with their associate factors to understand the complicated process of EMT in breast cancer progression and metastasis. Electrostatic potential surfaces have been analyzed that help in optimization of electrostatic interactions between the protein and its ligand. Therefore, understanding the biological implications underlying the EMT process through molecular biology with biocomputation and structural biology approaches will enable the development of new therapeutic strategies to sensitize tumors to conventional therapy and suppress their metastatic phenotype.

Urinary Ascites and Transient Intestinal Obstruction in a Preterm Infant: An Interesting Case of Posterior Urethral Valve

Posterior urethral valve (PUV) is the most common congenital cause of bladder outflow obstruction in male neonates. We report a preterm neonate with PUV who presented as nonimmune fetal hydrops with intestinal obstruction in the antenatal period. The mother of our patient is a 33-year-old woman who started her prenatal care at our hospital at 30 weeks' gestation. Her sonogram done at 32 weeks in our hospital revealed fetal hydrops. It showed polyhydramnios, mild pyelectasis of right kidney, normal left kidney, and fetal ascites. Amniocentesis revealed bile stained amniotic fluid. Ultrasound during the procedure showed dilated fetal bowel loops with increased echoes. Following delivery at 32 weeks postnatal exam showed ascites with absence of skin edema, pleural, or pericardial effusion. The abdominal sonogram showed distended urinary bladder and bilateral hydroureteronephrosis. Bladder catheterization was done which relieved the bladder outlet obstruction. Voiding cystourethrogram was done later which confirmed PUV and bilateral grade 5 vesicoureteral reflux. The formation of urinary ascites in PUV serves as a pop-off mechanism to relieve the intravesical and intrarenal pressure. When this happens by mechanisms other than bladder rupture, it can lead on to transient intestinal obstruction and hepatic synthetic defects.

Evolution of ligand-capped nanoparticle multilayers toward a near unique thickness

The structural evolution of thiol-capped Au-nanoparticle (AuNP) multilayers on a H-passivated Si substrate, formed through a Langmuir-Schaefer (LS) deposition process, has been investigated using complementary grazing incidence X-ray scattering techniques. The fractional coverage multilayers of AuNPs, formed through a multi-transfer process, are found to be quite unstable under ambient conditions. The thickness of these decreases with time and tends to saturate toward a near unique thickness (NUT ≈ 6 nm). Although initial low coverage and their instability create hindrance in the control and formation of desired 3D-nanostructures in the bottom-up approach, the formation of a NUT-layer, through time-evolution, is quite distinctive, thus interesting. It is clear from the evolution that the thermodynamically driven monolayer structures (of AuNPs) at the air-water interface become thermodynamically unstable when transferred sequentially onto the solid substrate. The thermal energy (kT) and the partial change in the substrate surface energy (Δγ) create the instability and induce diffusion in the AuNPs, which in the presence of a net attractive force towards the substrate (arising from anisotropic interaction of the top AuNPs with the other AuNPs and/or hydrophobic substrate) tries to create a thermodynamically favourable and relatively stable NUT-layer through reorganization for a different duration. This happens if the number of AuNPs is less than or equal to the maximum number that can be accommodated within the NUT. The value of the NUT mainly depends on the particle size and a kT-energy related fluctuation of particles. Furthermore, the formation of the NUT-layer indicates that the hydrophobic-hydrophobic interaction mediated net attraction towards the substrate is long range, while the hydrophilic-hydrophobic interaction mediated repulsion and/or kT-energy induced fluctuations are short range.

Database on spermatozoa transcriptogram of catagorised Frieswal crossbred (Holstein Friesian X Sahiwal) bulls

Bull spermatozoa contain different functional genes and many of them plays important roles in different stages of spermatogenesis, spermatozoa kinetics, fertilization as well as embryonic development. RNA deep sequencing is one of the preferred tools for absolute quantification of messenger RNA. The intention of the current study was to investigate the abundance of spermatozoal transcripts in categorized Frieswal (Holstein-Friesian X Sahiwal) crossbred bull semen through RNA deep sequencing. A total 1546561 and 1019308 numbers of reads were identified among good and poor quality bull spermatozoa based on their conception rate. Post mapping with Bos taurus reference genome identified 1,321,236 and 842,022 number of transcripts among good and poor quality RNA libraries, respectively. However, a total number of 3510 and 6759 functional transcripts were identified among good and poor quality bull spermatozoa, respectively. Most of the identified transcripts were related to spermatozoa functions, embryonic development and other functional aspects of fertilization. Wet laboratory validation of the top five selected transcripts (AKAP4, PRM1, ATP2B4, TRIM71 and SLC9B2) illustrated the significant (p < 0.01) level of expression in the good quality crossbred bull semen than the poor quality counterparts. The present study with comprehensive profiling of spermatozoal transcripts provides a useful non-invasive tool to understand the causes of as well as an effective way to predict male infertility in crossbred bulls.

Insights into the role of d-amino acid oxidase mutations in amyotrophic lateral sclerosis

Missense mutations in the coding region of d-amino acid oxidase (DAO) have been found in patients suffering from amyotrophic lateral sclerosis (ALS). Mutations primarily impair the enzymatic activity of DAO and cause neurodegeneration due to an abnormal accumulation of d-serine in the spinal cord. However, the structural and dynamic changes that lead to impaired enzymatic activity are not fully understood. We present here extensive molecular dynamics simulations of wild-type, and all reported ALS-associated DAO mutants to elucidate the plausible mechanisms of impaired enzymatic activity, a critical function needed for neuroprotection. Simulation results show that DAO mutations disrupt several key interactions with the active site residues and decrease the conformational flexibility of active site loop comprising 216 to 228 residues, necessary for substrate binding and product release. This conformational restriction of the active site loop in the mutants is mainly due to the distortion of critical salt bridge and hydrogen bond interactions compared with wild-type. Furthermore, binding free energy calculations show that DAO mutants have a lower binding affinity toward cofactor flavin adenine dinucleotide and substrate imino-serine than the wild-type. A closer look at the cofactor and substrate interaction profiles further show that DAO mutants have lost several critical interactions with the neighboring residues as compared with wild-type. Taken together, this study provides first-hand explanation of crucial structural features that lead to the loss of enzymatic function in DAO mutants and highlights the need of further genomic scans of patients with ALS to map the association of novel DAO variants in ALS pathophysiology.

Xylitol Production from Lignocellulosic Pentosans: A Rational Strain Engineering Approach toward a Multiproduct Biorefinery

Kluyveromyces marxianus IIPE453 can utilize biomass-derived fermentable sugars for xylitol and ethanol fermentation. In this study, the xylitol production in the native strain was improved by overexpression of endogenous d-xylose reductase gene. A suitable expression cassette harboring the gene of interest was constructed and incorporated in the native yeast. qPCR analysis demonstrated the 2.1-fold enhancement in d-xylose reductase transcript levels in the modified strain with 1.62-fold enhancement in overall xylitol yield without affecting its ethanol fermenting capacity. Material balance analysis on 2 kg of sugar cane bagasse-derived fermentable sugars illustrated an excess of 58.62 ± 0.15 g of xylitol production by transformed strain in comparison to the wild variety with similar ethanol yield. The modified strain can be suitably used as a single biocatalyst for multiproduct biorefinery application.

Non-inertial lift induced migration for label-free sorting of cells in a co-flowing aqueous two-phase system

We present a novel label-free passive microfluidic technique for isolation of cancer cells (EpCAM+ and CD45−) from peripheral blood mononuclear cells (PBMCs) (CD45+ and EpCAM−) in aqueous two-phase system (ATPS).