A novel strategy to avoid sensitivity loss in pooled testing for SARS-CoV-2 surveillance: validation using nasopharyngeal swab and saliva samples.

At the peak of the COVID-19 pandemic, pooled surveillance strategies were employed to alleviate the overwhelming demand for clinical testing facilities. A major drawback of most pooled-testing methods is the dilution of positive samples, which leads to a loss of detection sensitivity and the potential for false negatives. We developed a novel pooling strategy that compensates for the initial dilution with an appropriate concentration during nucleic acid extraction and real-time PCR. We demonstrated the proof of principle using laboratory-created 10-sample pools with one positive and corresponding individual positive samples by spiking a known amount of heat-inactivated SARS-CoV-2 into viral transport medium (VTM) or pooled negative saliva. No Ct difference was observed between a 10-sample pool with one positive vs. the corresponding individually analyzed positive sample by this method, suggesting that there is no detectable loss of sensitivity. We further validated this approach by using nasopharyngeal swab (NPS) specimens and showed that there is no loss of sensitivity. Serial dilutions of the virus were spiked into VTM and pooled with negative saliva in simulated 10-sample pools containing one positive to determine the LOD and process efficiency of this pooling methodology. The LOD of this approach was 10 copies/PCR, and the process efficiencies are ~95%-103% for N1 and ~87%-98% for N2 with samples in different matrices and with two different master mixes tested. Relative to TaqPath 1-step master mix, the TaqMan Fast Virus 1-Step master mix showed better sensitivity for the N2 assay, while the N1 assay showed no Ct difference. Our pooled testing strategy can facilitate large-scale, cost-effective SARS-CoV-2 surveillance screening and maintain the same level of sensitivity when analyzed individually or in a pool. This approach is highly relevant for public health surveillance efforts aimed at mitigating SARS-CoV-2 spread.

Transmission across non-HermitianPT-symmetric quantum dots and ladders.

A non-Hermitian (NH) region connected to semi-infinite Hermitian lattices acts either as a source or as a sink and the probability current is not conserved in a scattering typically. Even aPT-symmetric region that contains both a source and a sink does not lead to current conservation plainly. We propose a model and study the scattering across a NHPT-symmetric two-level quantum dot (QD) connected to two semi-infinite one-dimensional lattices in a special way so that the probability current is conserved. Aharonov-Bohm type phases are included in the model, which arise from magnetic fluxes (ℏϕL/e, ℏϕR/e) through two loops in the system. We show that whenϕL=ϕR, the probability current is conserved. We find that the transmission across the QD can be perfect in thePT-unbroken phase (corresponding to real eigenenergies of the isolated QD) whereas the transmission is never perfect in thePT-broken phase (corresponding to purely imaginary eigenenergies of the QD). The two transmission peaks have the same width only for special values of the fluxes (being odd multiples ofπℏ/2e). In the broken phase, the transmission peak is surprisingly not at zero energy. We give an insight into this feature through a four-site toy model. We extend the model to aPT-symmetric ladder connected to two semi-infinite lattices. We show that the transmission is perfect in unbroken phase of the ladder due to Fabry-Pérot type interference, that can be controlled by tuning the chemical potential. In the broken phase of the ladder, the transmission is substantially suppressed.

Implementing Pool-Based Surveillance Testing for SARS-CoV-2 at the Army Public Health Center Laboratory and across the Army Public Health Laboratory Enterprise.

With limited clinical resources, burgeoning testing requests from Army and other Service units to clinical laboratories, and the continued spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) throughout the military population, the Army Public Health Laboratory (APHL) Enterprise was tasked to establish surveillance testing capabilities for active duty military populations in an expedient manner. Following a proof-of-concept study conducted by Public Health Command-Pacific, Public Health Command-Europe was the first public health laboratory to offer the capability to assess for SARS-CoV-2 in pooled samples, followed closely by the Army Public Health Center (APHC) at Aberdeen Proving Grounds, MD, paralleling the spread of the SARS-CoV-2 virus from China to Europe to the continental US. The APHLs have selected pool sizes of up to 10 samples per pool based on the best evidence available at the time of method development and validation. Real-Time quantitative Reverse Transcriptase-Polymerase Chain Reaction (qRT-PCR) assays using RNA extracts from pooled nasopharyngeal swabs preserved in viral transport media were selected to assess the presence of SARS-CoV-2. The rapid development of initial surveillance testing capabilities depended on existing equipment in each laboratory, with a plan to implement full operational capability using additional staff and common high-throughput platforms. APHL Enterprise has successfully used existing resources to begin to address the changing and complex needs for COVID-19 testing within the Army population. Successful implementation of pooled surveillance testing at the APHC Laboratory has enabled more than 8,600 Soldiers to avoid clinical testing to date. The APHC Laboratory alone has tested over 10,000 samples and prevented approximately 8,600 soldiers from seeking testing with clinical diagnostic assays.

Statistical Optimization for Coproduction of Chitinase and Beta 1, 4-Endoglucanase by Chitinolytic Paenibacillus elgii PB1 Having Antifungal Activity.

A bacterial strain PB1 with antagonistic activity against pathogenic fungi was isolated from marine soil and was identified as Paenibacillus elgii based on phenotypic and genotypic characterization. The isolate showed good antifungal activity against "Aspergillus niger (MTCC 282), Trichophyton rubrum (MTCC 791), Microsporum gypseum (MTCC 2819), Candida albicans (MTCC 227), and Saccharomyces cerevisiae (MTCC 170)". Chitinase and beta 1, 4-endoglucanase are known for their capability to degrade fungal cell wall, thus we analyzed its productivity in PB1 strain using Plackett-Burman and Central Composite Design. The factors that affect the productivity of chitinase and beta 1, 4-endoglucanase were identified and optimized. A 7.77-fold increase (3.157 to 24.53 ± 1.33 U/mL) in chitinase and 7.422-fold increase (6.476 to 48.066 ± 0.676 U/mL) in beta 1, 4-endoglucanase versus basal medium was achieved. Chitinase and beta 1, 4-endoglucanase produced by Paenibacillus elgii strain PB1 represents the new source for biotechnological, medical, and agricultural applications.

Production of ß -cyclodextrin from pH and thermo stable Cyclodextrin Glycosyl Transferase, obtained from Arthrobacter mysorens and its evaluation as a drug carrier for Irbesartan.

Cyclodextrins (CDs) are carrier molecules produced by cyclization of α-1,4-glucans by Cyclodextrin Glycosyl Transferase (CGTase). These torus shaped molecules have hydrophobic cavity and hydrophilic shell making them useful in pharmaceutical, food, textile, pesticide and cosmetic industries. In this study, culture conditions for the production of CGTase by organism belonging to Arthrobacter genus obtained from a paddy field soil were optimized by single parameter mode. Soluble starch, yeast extract and magnesium sulphate played an important role in CGTase production. Percentage increase in CGTase yield under optimized conditions was 396.77%. The enzyme precipitated by 60% ammonium sulphate was purified using DEAE-sepharose. The molecular weight of the purified protein as determined by SDS-PAGE was 75 kDa. Purified CGTase was thermostable and stable over a wide pH range. Dissolution studies on ß -cyclodextrin-Irbesartan complex revealed that ß -CDs formed were useful in preparing immediate release oral dosage forms.

Pressure induced phase transitions and metallization of a neutral radical conductor.

The crystal structure and charge transport properties of the prototypal oxobenzene-bridged 1,2,3-bisdithiazolyl radical conductor 3a are strongly dependent on pressure. Compression of the as-crystallized α-phase, space group Fdd2, to 3-4 GPa leads to its conversion into a second or ß-phase, in which F-centering is lost. The space group symmetry is lowered to Pbn21, and there is concomitant halving of the a and b axes. A third or γ-phase, also space group Pbn21, is generated by further compression to 8 GPa. The changes in packing that accompany both phase transitions are associated with an "ironing out" of the ruffled ribbon-like architecture of the α-phase, so that consecutive radicals along the ribbons are rendered more nearly coplanar. In the ß-phase the planar ribbons are propagated along the b-glides, while in the γ-phase they follow the n-glides. At ambient pressure 3a is a Mott insulator, displaying high but activated conductivity, with σ(300 K) = 6 × 10(-3) S cm(-1) and E(act) = 0.16 eV. With compression beyond 4 GPa, its conductivity is increased by 3 orders of magnitude, and the thermal activation energy is reduced to zero, heralding the formation of a metallic state. High pressure infrared absorption and reflectivity measurements are consistent with closure of the Mott-Hubbard gap near 4-5 GPa. The results are discussed in the light of DFT calculations on the molecular and band electronic structure of 3a. The presence of a low-lying LUMO in 3a gives rise to high electron affinity which, in turn, creates an electronically much softer radical with a low onsite Coulomb potential U. In addition, considerable crystal orbital (SOMO/LUMO) mixing occurs upon pressurization, so that a metallic state is readily achieved at relatively low applied pressure.

A Fractional Factorial Design to Study the Effect of Process Variables on the Preparation of Hyaluronidase Loaded PLGA Nanoparticles.

The present study was initiated to understand the effect of PLGA concentration, PVA concentration, internal-external phase ratio, homogenization speed, and homogenization time on mean particle size, zeta potential, and percentage drug encapsulation using fractional factorial design. Using PLGA (50-50) as the carrier, hyaluronidase loaded PLGA nanoparticles were prepared using double emulsion solvent evaporation technique. The particle size was analyzed by dynamic light scattering technique and protein content by Lowry method. The study showed that homogenization speed as an independent variable had maximum effect on particle size and zeta potential. Internal-external phase volume ratio had maximum effect on drug encapsulation. Mean particle size also had high dependency on the combined effect of PVA concentration and phase volume ratio. Using fractional factorial design particle size of <400 nm, zeta potential of <-30 mV, and percentage encapsulation of 15-18% were achieved.

Reduced expression of ribosomal proteins relieves microRNA-mediated repression.

MicroRNAs (miRNAs) regulate physiological and pathological processes by inducing posttranscriptional repression of target messenger RNAs (mRNAs) via incompletely understood mechanisms. To discover factors required for human miRNA activity, we performed an RNAi screen using a reporter cell line of miRNA-mediated repression of translation initiation. We report that reduced expression of ribosomal protein genes (RPGs) dissociated miRNA complexes from target mRNAs, leading to increased polysome association, translation, and stability of miRNA-targeted mRNAs relative to untargeted mRNAs. RNA sequencing of polysomes indicated substantial overlap in sets of genes exhibiting increased or decreased polysomal association after Argonaute or RPG knockdowns, suggesting similarity in affected pathways. miRNA profiling of monosomes and polysomes demonstrated that miRNAs cosediment with ribosomes. RPG knockdowns decreased miRNAs in monosomes and increased their target mRNAs in polysomes. Our data show that most miRNAs repress translation and that the levels of RPGs modulate miRNA-mediated repression of translation initiation.

Optimization of cultural conditions for protease production by a fungal species.

Studies were carried out on a paddy soil fungal isolate identified to be a strain of Aspergillus niger from Manipal. The parameters that largely impact enzyme production viz., fermentation time, impeller speed, pH, temperature and nutrient supplements were studied. Optimization of production parameters for production of protease was done by the single-parameter mode. Casein served as substrate and proteolytic activity was estimated using Folin-Ciocalteau method at 660 nm. A maximum yield of 71.3 mg tyrosine/g casein substrate was produced in 96 h on a soluble starch medium at pH 4 in shake flask experiments. Production was carried out on a 3-liter fermenter and 40.7 mg of tyrosine was liberated/g of substrate. The enzyme was extracted with 50% ammonium sulfate and sodium dodecyl sulfate-Polyacrylamide gel electrophoresis showed two bands having mw 45.7 kDa and 38.5 kDa, respectively. The enzyme activity was found to be 147.84 U/ml.

Synergy of gatifloxacin with cefoperazone and cefoperazone-sulbactam against resistant strains of Pseudomonas aeruginosa.

Chequerboard and time-kill methods were used to compare the in vitro efficacies of the combinations gatifloxacin (GAT) with cefoperazone (CFP) and GAT with cefoperazone-sulbactam (CFP-SUL) against 58 clinical isolates of Pseudomonas aeruginosa. The combinations GAT+CFP and GAT+CFP-SUL were shown to be synergistic for 36.2 and 58.6 % of isolates tested, respectively, using the chequerboard method. Time-kill studies with 11 strains showed synergy in 54.5 % for the GAT+CFP combination and 72.7 % for the GAT+CFP-SUL combination. The agreement between these two methods was found to be 72-81 %. There was a significant difference in synergy between the two combinations tested (P=0.011).

NH3 gas sensing properties of nanocrystalline ZnO based thick films.

Zinc acetate derived precursor used in the present sol-gel synthesis of zinc oxide nanoparticles is described. The reaction product obtained before and after reflux of propanolic zinc acetate solution have been studied by UV-vis, photoluminescence and FT-IR studies which confirm the formation of oligomeric precursor Zn4O(Ac)6 (Ac=CH3COO). The formation of approximately 7 nm zinc oxide nanoparticles were confirmed by X-ray diffraction (XRD) and Transmission electron microscopic studies (TEM). The gaseous ammonia gas sensing characteristics of the nano-zinc oxide sensor showed high sensitivity compared to sensor fabricated with commercial zinc oxide powder.

Development and characterization of an immobilized human organic cation transporter based liquid chromatographic stationary phase.

Membranes from a stably transfected cell line that expresses the human organic cation 1 transporter (hOCT1) have been immobilized on the immobilized artificial membrane (IAM) liquid chromatographic stationary phase to form the hOCT1(+)-IAM stationary phase. Membranes from the parent cell line that does not express the hOCT1 were also immobilized to create the hOCT1(-)-IAM stationary phase. Columns were created using both stationary phases, and frontal displacement chromatography experiments were conducted using [(3)H]-methyl phenyl pyridinium ([(3)H]-MPP(+)) as the marker ligand and MPP(+), verapamil, quinidine, quinine, nicotine, dopamine and vinblastin as the displacers. The K(d) values calculated from the chromatographic studies correlated with previously reported K(i) values (r(2)=0.9987; p<0.001). The data indicate that the hOCT1(+)-IAM column can be used for the on-line determination of binding affinities to the hOCT1 and that these affinities are comparable to those obtained using cellular uptake studies. In addition, the chromatographic method was able to identify a previously undetected high affinity binding site for MPP(+) and to determine that hOCT1 bound (R)-verapamil to a greater extent than (S)-verapamil.

Metabolism of a novel phosphodiesterase-IV inhibitor (V11294) by human hepatic cytochrome P450 forms.

1. The metabolism of a novel phosphodiesterase-IV inhibitor (V11294) was studied in human liver microsomal and cytosol preparations and in cDNA-expressed human hepatic CYP forms. 2. Human liver microsomes, but not cytosol, catalysed the NADPH-dependent metabolism of V11294 to V10331 (formed by hydroxylation of the cyclopentyl ring), V10332 (N-desethyl V11294) and V11689 (formed by hydroxylation of the isopropyl side chain). In addition, smaller amounts of a secondary metabolite V11690 (which can be formed from either V10332 or V11689) were also produced. 3. Kinetic analysis of V11294 metabolism to V10331, V10332 and V11689 in two preparations of pooled human liver microsomes revealed average K(m) = 2.5, 8.1 and 3.9 micro M, respectively. 4. The metabolism of V11294 was determined with a characterized bank of 16 individual human liver microsomal preparations employing a V11294 substrate concentration of 8 micro M (i.e. approximately the K(m) for V10332 formation and around twice the K(m) for V10331 and V11689 formation). Good correlations (r(2) = 0.570-0.903) were observed between V10331, V10332 and V11689 formation and markers of CYP3A forms. In contrast, poorer correlations (r(2) = 0.0002-0.428) were observed with markers of CYP1A2, CYP2A6, CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP2E1 and CYP4A9/11. 5. Using human B-lymphoblastoid cell microsomes containing cDNA-expressed CYP forms, V11294 (8 micro M) was metabolized by cDNA-expressed CYP3A4 to V10331, V10332 and V11689, with lower amounts of V11690 also being formed. Lower rates of V11294 metabolism to some V11294 metabolites were also observed with cDNA-expressed CYP2C9, CYP2C19 and CYP2D6, whereas only very low or undetectable rates of V11294 metabolism were observed with cDNA-expressed CYP1A2, CYP2A6, CYP2B6, CYP2C8 and CYP2E1. 6. The metabolism of V11294 (8 micro M) to V10331, V10332 and V11689 was markedly inhibited by the CYP3A mechanism-based inhibitor troleandomycin. In contrast, V11294 metabolism was not significantly affected by inhibitors of CYP1A2, CYP2C9, CYP2D6 and CYP2E1 or by the CYP2C19 substrate S-mephenytoin. 7. In summary, by correlation analysis, chemical inhibition studies and the use of cDNA-expressed CYPs, V11294 metabolism in human liver to V10331, V10332 and V11689 appears to be primarily catalysed by CYP3A forms.

Identification of cytochrome P-450 isoforms responsible for cis-tramadol metabolism in human liver microsomes.

The metabolism of cis-tramadol has been studied in human liver microsomes and in cDNA-expressed human cytochrome P-450 (CYP) isoforms. Human liver microsomes catalyzed the NADPH-dependent metabolism of tramadol to the two primary tramadol metabolites, namely, O-desmethyl-tramadol (metabolite M1) and N-desmethyl-tramadol (metabolite M2). In addition, tramadol was also metabolized to two minor secondary metabolites (each comprising < or =3.0% of total tramadol metabolism), namely, N,N-didesmethyl-tramadol (metabolite M3) and N,O-didesmethyl-tramadol (metabolite M5). Kinetic analysis revealed that multiple CYP enzymes were involved in the metabolism of tramadol to both M1 and M2. For the high-affinity enzymes involved in M1 and M2 formation, K(m) values were 116 and 1021 microM, respectively. Subsequent reaction phenotyping studies were performed with a tramadol substrate concentration of 250 microM. In studies with characterized human liver microsomal preparations, good correlations were observed between tramadol metabolism to M1 and M2 and enzymatic markers of CYP2D6 and CYP2B6, respectively. Tramadol was metabolized to M1 by cDNA-expressed CYP2D6 and to M2 by CYP2B6 and CYP3A4. Tramadol metabolism in human liver microsomes to M1 and M2 was markedly inhibited by the CYP2D6 inhibitor quinidine and the CYP3A4 inhibitor troleandomycin, respectively. In summary, this study demonstrates that cis-tramadol can be metabolized to tramadol metabolites M1, M2, M3, and M5 in human liver microsomal preparations. By kinetic analysis and the results of the reaction phenotyping studies, tramadol metabolism in human liver is catalyzed by multiple CYP isoforms. Hepatic CYP2D6 appears to be primarily responsible for M1 formation, whereas M2 formation is catalyzed by CYP2B6 and CYP3A4.

Benzene and its phenolic metabolites produce oxidative DNA damage in HL60 cells in vitro and in the bone marrow in vivo.

Benzene, an important industrial chemical, is myelotoxic and leukemogenic in humans. It is metabolized by cytochrome P450 2E1 to various phenolic metabolites which accumulate in the bone marrow. Bone marrow contains high levels of myeloperoxidase which can catalyze the further metabolism of the phenolic metabolites to reactive free radical species. Redox cycling of these free radical species produces active oxygen. This active oxygen may damage cellular DNA (known as oxidative DNA damage) and induce genotoxic effects. Here we report the induction of oxidative DNA damage by benzene and its phenolic metabolites in HL60 cells in vitro and in the bone marrow of C57BL/6 x C3H F1 mice in vivo utilizing 8-hydroxy-2'-deoxyguanosine as a marker. HL60 cells (a human leukemia cell line) contain high levels of myeloperoxidase and were used as an in vitro model system. Exposure of these cells to phenol, hydroquinone, and 1,2,4-benzenetriol resulted in an increased level of oxidative DNA damage. An increase in oxidative DNA damage was also observed in the mouse bone marrow in vivo 1 h after benzene administration. A dose of 200 mg/kg benzene produced a 5-fold increase in the 8-hydroxydeoxyguanosine level. Combinations of phenol, catechol, and hydroquinone also resulted in significant increases in steady state levels of oxidative DNA damage in the mouse bone marrow but were not effective when administered individually. Administration of 1,2,4-benzenetriol alone did, however, result in a significant increase in oxidative DNA damage. This represents the first direct demonstration of active oxygen production by benzene and its phenolic metabolites in vivo. The conversion of benzene to phenolic metabolites and the subsequent production of oxidative DNA damage may therefore play a role in the benzene-induced genotoxicity, myelotoxicity, and leukemia.