Evaluation of Homology-Independent CRISPR-Cas9 Off-Target Assessment Methods.

The ability to alter genomes specifically by CRISPR-Cas gene editing has revolutionized biological research, biotechnology, and medicine. Broad therapeutic application of this technology, however, will require thorough preclinical assessment of off-target editing by homology-based prediction coupled with reliable methods for detecting off-target editing. Several off-target site nomination assays exist, but careful comparison is needed to ascertain their relative strengths and weaknesses. In this study, HEK293T cells were treated with Streptococcus pyogenes Cas9 and eight guide RNAs with varying levels of predicted promiscuity in order to compare the performance of three homology-independent off-target nomination methods: the cell-based assay, GUIDE-seq, and the biochemical assays CIRCLE-seq and SITE-seq. The three methods were benchmarked by sequencing 75,000 homology-nominated sites using hybrid capture followed by high-throughput sequencing, providing the most comprehensive assessment of such methods to date. The three methods performed similarly in nominating sequence-confirmed off-target sites, but with large differences in the total number of sites nominated. When combined with homology-dependent nomination methods and confirmation by sequencing, all three off-target nomination methods provide a comprehensive assessment of off-target activity. GUIDE-seq's low false-positive rate and the high correlation of its signal with observed editing highlight its suitability for nominating off-target sites for ex vivo CRISPR-Cas therapies.

Observation of Mode-Locked Spatial Laser Solitons.

A stable nonlinear wave packet, self-localized in all three dimensions, is an intriguing and much sought after object in nonlinear science in general and in nonlinear photonics in particular. We report on the experimental observation of mode-locked spatial laser solitons in a vertical-cavity surface-emitting laser with frequency-selective feedback from an external cavity. These spontaneously emerging and long-term stable spatiotemporal structures have a pulse length shorter than the cavity round-trip time and may pave the way to completely independent cavity light bullets.

Mapping the dynamic complexity of a semiconductor laser with optical feedback using permutation entropy.

A semiconductor laser with delayed optical feedback is an experimental implementation of a nominally infinite dimensional dynamical system. As such, time series analysis of the output power from this laser system is an excellent test of complexity analysis tools, as applied to experimental data. Additionally, the systematic characterization of the range and variation in complexity that can be obtained in the output power from the system, which is available to be used in applications like secure communication, is of interest. Output power time series from a semiconductor laser system, as a function of the optical feedback level and the laser injection current, have been analyzed for complexity using permutation entropy. High resolution maps of permutation entropy as a function of optical feedback level and injection current have been achieved for the first time. This confirms prior research that identifies a coherence collapse region which is found to be uninterrupted with respect to any embedded islands with different dynamics. The results also show new observations of low optical feedback dynamics which occur in a region below that for coherence collapse. The map of the complexity shows a strong dependence on the delay time used in the permutation entropy calculation. Short delay times, which sample information at the complete measurement bandwidth, produce maps with drastically different systematic variation in complexity throughout the coherence collapse region, compared to maps generated with a delay time that matches the optical feedback delay. Evaluating the complexity with a permutation entropy delay equal to the external cavity delay produces results consistent with the notion of weak/strong chaos, as well as categorizing the dynamics as being of high complexity where the external cavity delay time is harder to identify. These are both desirable features for secure communication applications. The results also show permutation entropy as a function of delay time can be used to detect key frequencies driving the dynamics, including any that may exist due to, or arise from, technicalities of device fabrication and/or noise. A more complete insight into complexity as measured by permutation entropy is gained by considering multiple delay times.

Stability of the nonlinear dynamics of an optically injected VCSEL.

Automated protocols have been developed to characterize time series data in terms of stability. These techniques are applied to the output power time series of an optically injected vertical cavity surface emitting laser (VCSEL) subject to varying injection strength and optical frequency detuning between master and slave lasers. Dynamic maps, generated from high resolution, computer controlled experiments, identify regions of dynamic instability in the parameter space.

Variable pulse repetition frequency output from an optically injected solid state laser.

An optically injected solid state laser (OISSL) system is known to generate complex nonlinear dynamics within the parameter space of varying the injection strength of the master laser and the frequency detuning between the master and slave lasers. Here we show that within these complex nonlinear dynamics, a system which can be operated as a source of laser pulses with a pulse repetition frequency (prf) that can be continuously varied by a single control, is embedded. Generation of pulse repetition frequencies ranging from 200 kHz up to 4 MHz is shown to be achievable for an optically injected Nd:YVO4 solid state laser system from analysis of prior experimental and simulation results. Generalizing this to other optically injected solid state laser systems, the upper bound on the repetition frequency is of order the relaxation oscillation frequency for the lasers. The system is discussed in the context of prf versatile laser systems more generally. Proposals are made for the next generation of OISSLs that will increase understanding of the variable pulse repetition frequency operation, and determine its practical limitations. Such variable prf laser systems; both low powered, and, higher powered systems achieved using one or more optical power amplifier stages; have many potential applications from interrogating resonance behaviors in microscale structures, through sensing and diagnostics, to laser processing.

Responses to a conjugate pneumococcal vaccine in preterm infants immunized at 2, 3, and 4 months of age.

Preterm infants are at an increased risk of invasive pneumococcal disease infection and, additionally, have a diminished response to Haemophilus influenzae type b (Hib) conjugate vaccines. There are little data examining the response of preterm infants to a seven-valent pneumococcal conjugate vaccine (PCV7). We examined the responses of preterm infants immunized at 2, 3, and 4 months of age to PCV7. A total of 133 preterm and 54 term infants were immunized with PCV7 and the Neisseria meningitidis group C (MCC), diphtheria, tetanus, pertussis, polio, and Hib vaccines. Pneumococcal serotype-specific IgG was measured by enzyme-linked immunosorbent assay (ELISA) pre- and postimmunization and at 12 months or following a booster of PCV7. Term and preterm responses were compared using linear and logistic regression analyses. Term infants had higher preimmunization geometric mean concentrations (GMCs) for all serotypes. Preterm infants had lower postimmunization GMCs for serotype 23F. Gestational age affected postimmunization GMCs for serotypes 4, 6B, and 23F. Preterm infants were as likely to have levels of ≥0.35 µg/ml as term infants for all serotypes except 23F. The proportions of infants with titers of ≥0.35 µg/ml for all 7 serotypes were comparable between groups. A total of 28 of 29 term infants who received a booster had levels of ≥0.35 µg/ml for all serotypes. One infant had undetectable levels for serotype 6B. Of the 32 preterm infants boosted, 9 had levels of <0.35 µg/ml for 1 serotype, and 1 had levels of <0.35 µg/ml for 2 serotypes. In nonboosted infants, GMCs for all serotypes except 6B had fallen by 12 months of age. These results support the need for a booster dose in the second year of life.

Nonlinear dynamics of semiconductor lasers with feedback and modulation.

The nonlinear dynamics of two semiconductor laser systems: (i) with optical feedback, and (ii) with optical feedback and direct current modulation are evaluated from multi-GHz-bandwidth output power time-series. Animations of compilations of the RF spectrum (from the FFT of the time-series) as a function of optical feedback level, injection current and modulation signal strength is demonstrated as a new tool to give insight into the dynamics. The results are contrasted with prior art and new observations include fine structure in the RF spectrum at low levels of optical feedback and non-stationary switching between periodic and chaotic dynamics for some sets of laser system parameters. Correlation dimension analysis successfully identifies periodic dynamics but most of the dynamical states are too complex to be extracted using standard algorithms.

Immunogenicity of a heptavalent conjugate pneumococcal vaccine administered concurrently with a combination diphtheria, tetanus, five-component acellular pertussis, inactivated polio, and Haemophilus influenzae type B vaccine and a meningococcal group C conjugate vaccine at 2, 3, and 4 months of age.

The immunogenicities of conjugate pneumococcal vaccines have been demonstrated when they are administered at 2, 3, and 4 months of age. There is a paucity of data on the immunogenicity of this vaccine when it is administered concurrently with other vaccines in the primary immunization schedule of the United Kingdom. We immunized 55 term infants at 2, 3, and 4 months of age with the seven-valent pneumococcal conjugate vaccine (PCV7), the meningococcal group C conjugate (MCC) vaccine, and the diphtheria, tetanus, five-component acellular pertussis, inactivated polio, and Haemophilus influenzae type b (DTaP(5)/IPV/Hib-TT) vaccine. The immune responses to the H. influenzae type b (Hib), MCC, and tetanus vaccines were measured at 2, 5, and 12 months of age; and the immune responses to PCV7 were measured at 2 and 5 months and then either at 12 months or following a 4th dose of PCV7. There were increases in the geometric mean concentrations (GMCs) of all antigens postimmunization. Greater than or equal to 90% of the infants achieved putatively protective levels postimmunization for all vaccine antigens except pneumococcal serotype 6B and Hib. The GMCs of the PCV7 serotypes increased following a 4th dose, although one infant had not reached putative levels of protection against serotype 6B. In conclusion, when infants were vaccinated according to the schedule described above, they had lower postprimary immunization responses to Hib, meningococcus group C capsular polysaccharide, and pneumococcal serotype 6B than the responses demonstrated by use of the other schedules. Despite this finding, there was a good response following a 4th dose of PCV7.

Hybrid electronic/optical synchronized chaos communication system.

A hybrid electronic/optical system for synchronizing a chaotic receiver to a chaotic transmitter has been demonstrated. The chaotic signal is generated electronically and injected, in addition to a constant bias current, to a semiconductor laser to produce an optical carrier for transmission. The optical chaotic carrier is photodetected to regenerate an electronic signal for synchronization in a matched electronic receiver The system has been successfully used for the transmission and recovery of a chaos masked message that is added to the chaotic optical carrier. Past demonstrations of synchronized chaos based, secure communication systems have used either an electronic chaotic carrier or an optical chaotic carrier (such as the chaotic output of various nonlinear laser systems). This is the first electronic/optical hybrid system to be demonstrated. We call this generation of a chaotic optical carrier by electronic injection.

Automated correlation dimension analysis of optically injected solid state lasers.

Nonlinear lasers are excellent systems from which to obtain high signal-to-noise experimental data of nonlinear dynamical variables to be used to develop and demonstrate robust nonlinear dynamics analysis techniques. Here we investigate the dynamical complexity of such a system: an optically injected Nd:YVO(4) solid state laser. We show that a map of the correlation dimension as a function of the injection strength and frequency detuning, extracted from the laser output power time-series data, is an excellent mirror of the dynamics map generated from a theoretical model of the system. An automated computational protocol has been designed and implemented to achieve this. The correlation dimension map is also contrasted with prior research that mapped the peak intensity of the output power as an experimentally accessible measurand reflecting the dynamical state of the system [Valling et al., Phys. Rev. A 72, 033810 (2005)].

The quest for Factor VIIa exosite inhibitors.

Coagulation proteases are involved in a highly orchestrated proteolytic cascade which is essential for haemostasis and blood clotting. In particular, the initiator of the coagulation cascade, Factor VIIa, binds to its cofactor, tissue factor, and its substrate, Factor X, via exosite interactions to form a ternary catalytic complex named extrinsic Xase. These exosite interactions have also been shown to allosterically induce the active conformation of the catalytic site of Factor VIIa. We have developed a direct continuous fluorescence polarization-based extrinsic Xase assay, which has been used to screen in excess of 1 million structurally diverse low-molecular-mass compounds as a potential starting point for the development of anticoagulants. The primary screen hits were categorized with deconvolution assays into either active-site or exosite inhibitors. The latter category of hits displayed both competitive and uncompetitive modalities of inhibition with respect to Factor X activation. An uncompetitive mechanism of action is of particular interest as it offers a hypothetical inhibitory advantage in the context of inhibiting a proteolytic cascade such as the blood coagulation pathway.

A comparison of the beta-D-xyloside, odiparcil, to warfarin in a rat model of venous thrombosis.

BACKGROUND: A significant need exists for new chronic oral anticoagulation therapies to replace warfarin. Previous studies have shown that beta-D-xylosides, which prime glycosaminoglycan (GAG) synthesis, have antithrombin and antithrombotic activity. In the following report, a new orally active beta-D-xyloside (odiparcil) has been characterized in a rat model of venous thrombosis and its efficacy and bleeding liability compared to warfarin. Additionally, studies were conducted to investigate odiparcil's ex vivo antithrombin and antiplatelet activity, and also to explore the potential utility of protamine sulfate as a neutralizing agent. METHODS AND RESULTS: In vivo thrombosis studies were conducted in a rat inferior vena cava model, and bleeding studies in a rat tail transection model. Following oral dosing, warfarin and odiparcil produced dose-related suppression of thrombus formation. A therapeutically relevant dose of warfarin in this model (international normalized ratio; INR 3.0) achieved approximately 65% inhibition of thrombus formation. Warfarin caused dose-related significant increases in bleeding indices. Odiparcil antithrombotic activity was limited by its mechanism to a maximum suppression of thrombus formation of 65-70%, and did not prolong bleeding indices. Additionally, odiparcil-induced heparin cofactor II (HCII)-dependent antithrombin activity was shown to be a function of dermatan sulfate-like GAG production. Other than thrombin-related effects, no odiparcil effects on platelet function were observed. In antidote studies, it was demonstrated that odiparcil-induced antithrombotic activity could be partially neutralized by protamine sulfate. CONCLUSIONS: These experiments suggest that an antithrombotic approach based upon xyloside induction of circulating GAGs may have the potential to approximate the efficacy of warfarin and yet with a reduced risk to hemostasis.

P2X1 stimulation promotes thrombin receptor-mediated platelet aggregation.

P2X1 receptors are ATP-gated channel demonstrated to be involved in multiple platelet responses, although in vitro analysis has been complicated by the effects of rapid desensitization. To further investigate potential roles of P2X1 receptors in platelet activation, the current study employed methods which maximally preserved P2X1 functionality. In preliminary in vivo studies, P2X1-deficiency reduced thrombus formation following the laser-induced, but not FeCl3-induced injury. Given the multiple potential mechanisms involved in thrombus formation in vivo, including tissue-factor/thrombin generation pathways, subsequent studies were designed to investigate the effects of P2X1 inhibition or stimulation on platelet activation in vitro; specifically, the interaction of P2X1 with thrombin receptor stimulation. Aggregation initiated by low/threshold levels of a protease-activated receptor (PAR)4 agonist was reduced in P2X1-deficient murine platelets, and inhibition of P2X1 in wild-type platelets similarly reduced PAR4-mediated aggregation. In human platelets, aggregation to low/threshold stimulation of PAR1 was inhibited with the P2X1 antagonist MRS2159. In addition, P2X1 stimulation primed human platelet responses, such that subsequent sub-threshold PAR1 responses were converted into significant aggregation. Selective ADP receptor inhibitors attenuated P2X1-mediated priming, suggesting that the synergy between P2X1 and sub-threshold PAR1 stimulation was in part because of enhanced granular release of ADP. Overall, the present study defines a novel interaction between platelet P2X1 and thrombin receptors, with P2X1 functioning to amplify aggregation responses at low levels of thrombin receptor stimulation.

Correlation dimension signature of wideband chaos synchronization of semiconductor lasers.

Chaos data analysis has been performed on the chaotic output power time series data from a synchronized transmitter-receiver pair of semiconductor lasers. The system uses an asymmetric, bidirectional coupling configuration between the master (transmitter), which is a laser diode with optical feedback, and a stand-alone slave semiconductor laser. The correlation dimension of the chaotic time series has a minimum value of 4, which was obtained from high-bandwidth measurements. The correlation dimensions for both the master and the synchronized slave are identical when the cross-correlation coefficient of the synchronized chaos is above 0.9. These results establish correlation dimension analysis as an effective tool for the determination of the quality of wideband chaos synchronization.

Severe factor XI deficiency caused by a Gly555 to Glu mutation (factor XI-Glu555): a cross-reactive material positive variant defective in factor IX activation.

During normal hemostasis, the coagulation protease factor (F)XIa activates FIX. Hereditary deficiency of the FXIa precursor, FXI, is usually associated with reduced FXI protein in plasma, and circulating dysfunctional FXI variants are rare. We identified a patient with < 1% normal plasma FXI activity and normal levels of FXI antigen, who is homozygous for a FXI Gly555 to Glu substitution. Gly555 is two amino acids N-terminal to the protease active site serine residue, and is highly conserved among serine proteases. Recombinant FXI-Glu555 is activated normally by FXIIa and thrombin, and FXIa-Glu555 binds activated factor IX similarly to wild type FXIa (FXIa(WT)). When compared with FXIa(WT), FXIa-Glu555 activates factor IX at a greatly reduced rate ( approximately 400-fold), and is resistant to inhibition by antithrombin. Interestingly, FXIa(WT) and FXIa-Glu555 cleave the small tripeptide substrate S-2366 with comparable k(cat)s. Modeling indicates that the side chain of Glu555 significantly alters the electrostatic charge around the active site, and would sterically interfere with the interaction between the FXIa S2' site and the P2' residues on factor IX and antithrombin. FXI-Glu555 is the first reported example of a naturally occurring FXI variant with a significant defect in FIX activation.

Potentiation of platelet activation through the stimulation of P2X1 receptors.

The platelet P2X1 purinergic receptor is a ligand-gated ion channel that responds to ATP. The precise role of P2X1 in platelet function is unknown, though stimulation with the P2X1 agonist alpha,beta-Me-ATP is known to result in platelet shape change through elevation of calcium levels. The aim of the present study was to examine further the effects of P2X1 stimulation on platelet activation. Stimulation of P2X1 with alpha,beta-Me-ATP resulted in shape change and small aggregate formation in heparin-anticoagulated platelet preparations. Given the ability of heparin to potentiate platelet activation, subsequent experiments were performed in hirudin. In these platelet preparations, aggregate formation in response to alpha,beta-Me-ATP alone was less than that observed in heparin; however, alpha,beta-Me-ATP significantly potentiated platelet aggregate formation when added in conjunction with other weak platelet agonists [epinephrine or thrombopoietin (TPO)]. Platelet aggregate formation was confirmed by single platelet loss (microaggregate formation), microscopy, and light transmittance studies. Further, the P2X1 antagonist MRS-2159 inhibited platelet shape change and aggregation responses induced by alpha,beta-Me-ATP. Overall, this study demonstrates that P2X1 stimulation can induce/potentiate platelet activation in combination with other platelet agonists. These results are the first demonstration of platelet aggregation mediated through direct P2X1 stimulation, supporting a role for this receptor in regulating platelet activation.

Center for Synchrotron Biosciences' U2B beamline: an international resource for biological infrared spectroscopy.

A synchrotron infrared (IR) beamline, U2B, dedicated to the biomedical and biological sciences has been constructed and is in operation at the National Synchrotron Light Source (NSLS) of Brookhaven National Laboratory. The facility is operated by the Center for Synchrotron Biosciences of the Albert Einstein College of Medicine in cooperation with the NSLS. Owing to the broadband nature of the synchrotron beam with brightness 1000 times that of conventional sources, Fourier transform IR spectroscopy experiments are feasible on diffraction-limited sample areas at high signal-to-noise ratios and with relatively short data-acquisition times. A number of synchrotron IR microscopy experiments that have been performed in the mid-IR spectral range (500-5000 cm(-1)) are summarized, including time-resolved protein-folding studies in the microsecond time regime, IR imaging of neurons, bone and other biological tissues, as well as imaging of samples of interest in the chemical and environmental sciences. Owing to the high flux output of this beamline in the far-IR region (50-500 cm(-1)), investigations of hydrogen bonding and dynamic molecular motions of biomolecules have been carried out from 10 to 300 K using a custom-made cryostat and an evacuated box. This facility is intended as an international resource for biological IR spectroscopy fully available to outside users based on competitive proposal.

Functional analysis of the molecular factors controlling Qa1-mediated protection of target cells from NK lysis.

CD94/NKG2 receptors on mouse NK cells recognize the nonclassical class I molecule Qa1 and can deliver inhibitory signals that prevent NK cells from lysing Qa1-expressing cells. However, the exact circumstances under which Qa1 protects cells from NK lysis and, in particular, the role of the dominant Qa1-associated peptide, Qdm, are unclear. In this study, we examined in detail the lysis of Qa1-expressing cells by fetal NK cells that express CD94/NKG2 receptors for Qa1 but that lack receptors for classical class I molecules. Whereas mouse L cells and human C1R cells transfected with Qa1 were resistant to lysis by these effectors, Qa1-transfected TAP-deficient human T2 cells showed no resistance despite expressing high levels of surface Qa1. However, these cells could be efficiently protected by exposure to low concentrations of Qdm peptide or certain Qdm-related peptides. By contrast, even prolonged exposure of TAP-deficient RMA/S cells to high doses of Qdm peptide failed to induce levels of surface Qa1 detectable with a Qa1-specific mAb or to protect them from NK lysis, although such treatment induced sensitivity to lysis by Qa1-specific CTL. Collectively, these findings indicate that high surface expression of Qa1 is necessary but not sufficient for protection, and that effective protection requires the expression of sufficient levels of suitable Qa1-peptide complexes to overcome activatory signals. Results obtained with a series of substituted Qdm peptides suggest that residues at positions 3, 4, 5, and 8 of the Qdm sequence, AMAPRTLLL, are important for recognition of Qa1-Qdm complexes by inhibitory CD94/NKG2 receptors.

Comparing the antithrombotic efficacy of a humanized anti-factor IX(a) monoclonal antibody (SB 249417) to the low molecular weight heparin enoxaparin in a rat model of arterial thrombosis.

A humanized inhibitory anti-factor IX(a) antibody (SB 249417) has been compared to enoxaparin (Lovenox) in a rat model of arterial thrombosis. Pretreatment of rats with either SB 249417 (3.0 mg/kg, i. v.) or enoxaparin (30.0 mg/kg, i.v. or s.c.) resulted in comparable and significant reductions in thrombus formation. However, the efficacious dose of enoxaparin resulted in >30-fold increase in the aPTT over baseline, while the efficacious dose of SB 249417 prolonged the aPTT by only approximately 3-fold. Additionally, pretreatment with SB 249417 resulted in sustained blood flow and arterial patency throughout the experiment in >80% of rats treated. In contrast, <30% of rats pretreated with enoxaparin remained patent throughout the experiment. The data in this report indicate that the selective inhibition of factor IX(a) with the monoclonal antibody SB 249417 produces a superior antithrombotic profile to that of the low molecular weight heparin enoxaparin.