Direct interrogation of the role of H3K9 in metazoan heterochromatin function.

A defining feature of heterochromatin is methylation of Lys9 of histone H3 (H3K9me), a binding site for heterochromatin protein 1 (HP1). Although H3K9 methyltransferases and HP1 are necessary for proper heterochromatin structure, the specific contribution of H3K9 to heterochromatin function and animal development is unknown. Using our recently developed platform to engineer histone genes in Drosophila, we generated H3K9R mutant flies, separating the functions of H3K9 and nonhistone substrates of H3K9 methyltransferases. Nucleosome occupancy and HP1a binding at pericentromeric heterochromatin are markedly decreased in H3K9R mutants. Despite these changes in chromosome architecture, a small percentage of H3K9R mutants complete development. Consistent with this result, expression of most protein-coding genes, including those within heterochromatin, is similar between H3K9R and controls. In contrast, H3K9R mutants exhibit increased open chromatin and transcription from piRNA clusters and transposons, resulting in transposon mobilization. Hence, transposon silencing is a major developmental function of H3K9.

Supermode noise mitigation and repetition rate control in harmonic mode-locked fiber laser implemented through the pulse train interaction with co-lased CW radiation.

We report on new, to the best of our knowledge, techniques enabling both the mitigation of supermode laser noise and highly precise setting of the pulse repetition rate (PRR) in a soliton harmonically mode-locked (HML) fiber laser employing nonlinear polarization evolution (NPE). The principle of operation relies on resonant interaction between the soliton pulses and a narrowband continuous wave (CW) component cooperatively generated within the same laser cavity. In contrast to our recent findings [Opt. Lett.46, 5747 (2021)10.1364/OL.441630 and Opt. Lett.46, 5687 (2021)10.1364/OL.443042], the new methods are implemented through the specific adjustment of the HML laser cavity only and do not require the use of an external tunable CW laser source.

Supermode noise mitigation and repetition rate control in a harmonic mode-locked fiber laser implemented through the pulse train interaction with co-lased CW radiation: publisher's note.

This publisher's note contains corrections to Opt. Lett.47, 5236 (2022)10.1364/OL.472780.

Chromatin conformation and transcriptional activity are permissive regulators of DNA replication initiation in Drosophila.

Chromatin structure has emerged as a key contributor to spatial and temporal control over the initiation of DNA replication. However, despite genome-wide correlations between early replication of gene-rich, accessible euchromatin and late replication of gene-poor, inaccessible heterochromatin, a causal relationship between chromatin structure and replication initiation remains elusive. Here, we combined histone gene engineering and whole-genome sequencing in Drosophila to determine how perturbing chromatin structure affects replication initiation. We found that most pericentric heterochromatin remains late replicating in H3K9R mutants, even though H3K9R pericentric heterochromatin is depleted of HP1a, more accessible, and transcriptionally active. These data indicate that HP1a loss, increased chromatin accessibility, and elevated transcription do not result in early replication of heterochromatin. Nevertheless, a small amount of pericentric heterochromatin with increased accessibility replicates earlier in H3K9R mutants. Transcription is de-repressed in these regions of advanced replication but not in those regions of the H3K9R mutant genome that replicate later, suggesting that transcriptional repression may contribute to late replication. We also explored relationships among chromatin, transcription, and replication in euchromatin by analyzing H4K16R mutants. In Drosophila, the X Chromosome gene expression is up-regulated twofold and replicates earlier in XY males than it does in XX females. We found that H4K16R mutation prevents normal male development and abrogates hyperexpression and earlier replication of the male X, consistent with previously established genome-wide correlations between transcription and early replication. In contrast, H4K16R females are viable and fertile, indicating that H4K16 modification is dispensable for genome replication and gene expression.

Brillouin-like amplification in rare-earth-doped optical fibers.

We present a theoretical formalism to describe the amplification of two monochromatic waves counter-propagating in a rare-earth-doped optical fiber amplifier. Interaction of the waves through a dynamical population inversion grating inscribed in the active fiber by the waves during their amplification results in a strong power transfer from one wave to another providing a preferable amplification of one wave at the expense of another. In this sense, the effect is similar to stimulated Brillouin scattering and is expected to be observed with both pumped and unpumped rare-earth-doped fibers possessing a finite polarizability difference between the excited and ground states.

Seeded optical parametric generation in CdSiP2 pumped by a Raman fiber amplifier at 1.24 µm.

We report a seeded optical parametric generator (OPG) producing tunable radiation from 4.2-4.6 µm. The seeded OPG employs a 13 mm long CdSiP2 (CSP) crystal cut for non-critical phase-matching, pumped by a nanosecond-pulsed, MHz repetition rate Raman fiber amplifier system at 1.24 µm. A filtered, continuous-wave fiber supercontinuum source at 1.72 µm is used as the seed. The source generates up to 0.25 W of mid-infrared (MIR) idler power with a total pump conversion of 42% (combined signal and idler).

Nanosecond pulsed 620 nm source by frequency-doubling a phosphosilicate Raman fiber amplifier.

We demonstrate a nanosecond pulsed source at 620 nm with watt-level average power by frequency-doubling a 1240 nm phosphosilicate Raman fiber amplifier. A gain-switched laser diode operating at 1064 nm is amplified in an ytterbium fiber master oscillator power amplifier system and then converted to 1240 nm using a phosphosilicate Raman fiber amplifier with a conversion efficiency of up to 66%. The Raman fiber amplifier is seeded with a continuous-wave 1240 nm laser diode to obtain narrow-linewidth radiation, which is subsequently frequency-doubled in a periodically poled lithium tantalate crystal. A maximum average power of 1.5 W is generated at 620 nm, corresponding to a pulse energy of 300 nJ at a repetition rate of 5 MHz. The source has excellent beam quality (M2≤1.16) and an optical efficiency (1064 nm to 620 nm) of 20%, demonstrating an effective architecture for generating red pulsed light for biomedical imaging applications.

Highly efficient nanosecond 560 nm source by SHG of a combined Yb-Raman fiber amplifier.

We demonstrate a nanosecond 560 nm pulse source based on frequency-doubling the output of a combined Yb-Raman fiber amplifier, achieving a pulse energy of 2.0 µJ with a conversion efficiency of 32% from the 976 nm pump light. By introducing a continuous-wave 1120 nm signal before the cladding pumped amplifier of a pulsed Yb:fiber master oscillator power amplifier system operating at 1064 nm, efficient conversion to 1120 nm occurs within the fiber amplifier due to stimulated Raman scattering. The output of the combined Yb-Raman amplifier is frequency-doubled to 560 nm using a periodically poled lithium tantalate crystal with a conversion efficiency of 47%, resulting in an average power of 3.0 W at a repetition rate of 1.5 MHz. The 560 nm pulse duration of 1.7 ns and the near diffraction-limited beam quality (M2≤1.18) make this source ideally suited to biomedical imaging applications such as optical-resolution photoacoustic microscopy and stimulated emission depletion microscopy.

High average power parametric wavelength conversion at 3.31-3.48 m in MgO:PPLN.

We present results of high average power mid-infrared (mid-IR) generation employing synchronized nanosecond pulsed ytterbium and erbium fiber amplifier systems using periodically poled lithium niobate. We generate greater than 6 W of mid-IR radiation tunable in wavelength between 3.31-3.48 µm, at power conversion efficiencies exceeding 75%, with near diffraction limited beam quality (M2 = 1.4). Numerical modeling is used to verify the experimental results in differing pump depletion regimes.

Erasure of fear memories is prevented by Nogo Receptor 1 in adulthood.

Critical periods are temporary windows of heightened neural plasticity early in development. For example, fear memories in juvenile rodents are subject to erasure following extinction training, while after closure of this critical period, extinction training only temporarily and weakly suppresses fear memories. Persistence of fear memories is important for survival, but the inability to effectively adapt to the trauma is a characteristic of post-traumatic stress disorder (PTSD). We examined whether Nogo Receptor 1 (NgR1) regulates the plasticity associated with fear extinction. The loss of NgR1 function in adulthood eliminates spontaneous fear recovery and fear renewal, with a restoration of fear reacquisition rate equal to that of naive mice; thus, mimicking the phenotype observed in juvenile rodents. Regional gene disruption demonstrates that NgR1 expression is required in both the basolateral amygdala (BLA) and infralimbic (IL) cortex to prevent fear erasure. NgR1 expression by parvalbumin expressing interneurons is essential for limiting extinction-dependent plasticity. NgR1 gene deletion enhances anatomical changes of inhibitory synapse markers after extinction training. Thus, NgR1 robustly inhibits elimination of fear expression in the adult brain and could serve as a therapeutic target for anxiety disorders, such as PTSD.

Quantification of regional aerosol deposition patterns as a function of aerodynamic particle size in rhesus macaques using PET/CT imaging.

Aerosol aerodynamic particle size is known to affect deposition patterns of inhaled aerosol particles, as well as the virulence of inhaled bioaerosol particles. While a significant amount of work has been performed to describe the deposition of aerosol particles in the human respiratory tract, only a limited amount of work has been performed to describe the deposition of aerosol particles in the respiratory tract of nonhuman primates, an animal model commonly utilized in pharmacological and toxicological studies, especially in the biodefense field. In this study, anesthetized rhesus macaques inhaled radiolabeled aerosols with MMADs of 1.7, 3.6, 7.4 and 11.8 µm to characterize regional deposition patterns. The results demonstrate that the regional deposition pattern shifts as particle size increases, with greater deposition in more proximal regions of the respiratory tract and decreased deposition in the pulmonary region. The results of this study extend the findings of previous studies which demonstrated a similar shift in the deposition pattern as a function of particle size by providing greater resolution of deposition patterns. These data on regional deposition patterns provide a starting point to begin to explore potential mechanisms responsible for the differences in virulence of infectious bioaerosols as a function of particle size and deposition pattern reported in previous studies. Additionally, the data are useful to assess the performance of various deposition models that have been published in the literature.

Highly efficient mid-infrared difference-frequency generation using synchronously pulsed fiber lasers.

We report the development of a high average power, picosecond-pulse, mid-infrared source based on difference-frequency generation (DFG) of two synchronous master oscillator power fiber amplifier systems. The generated idler can be tuned over the range 3.28-3.45 µm delivering greater than 3.4 W of average power, with a maximum pump to total DFG power conversion efficiency of 78%. The benefits of a synchronously pumped scheme, compared to CW seeding of DFG sources, are discussed.

Fiber-integrated frequency-doubling of a picosecond Raman laser to 560 nm.

We report the development of a fiber-integrated picosecond source at 560 nm by second harmonic generation of a Raman fiber laser. A picosecond ytterbium master oscillator power fiber amplifier is used to pulse-pump a Raman amplifier, which is seeded by a continuous wave distributed feedback laser diode operating at 1120 nm. The pulse train generated at 1120 nm is frequency-doubled in a fiber-coupled periodically-poled lithium niobate crystal module, producing 450 mW of average power at 560 nm with a pulse duration of 150 ps at a repetition rate of 47.5 MHz. The near diffraction-limited (M(2) = 1.02) collimated output beam is ideal for super-resolution microscopy applications.

Duration-tunable picosecond source at 560 nm with watt-level average power.

A pulse source at 560 nm that is tunable in duration between 50 ps and 2.7 ns with >1 W of average power and near diffraction-limited beam quality is demonstrated. The source is based on efficient (up to 50%) second-harmonic generation in a periodically poled lithium tantalate crystal of a linearly polarized fiber-integrated Raman amplifier operating at 1120 nm. A duration-tunable ytterbium master-oscillator power-fiber amplifier is used to pulse-pump the Raman amplifier, which is seeded by a continuous-wave distributed-feedback laser diode at 1120 nm. The performance of the system using two different master oscillator schemes is compared. A pulse energy of up to 765 nJ is achieved with a conversion efficiency of 25% from the ytterbium fiber pump, demonstrating a compact and turn-key architecture for obtaining high peak-power radiation at 560 nm.

Fiber grating compression of giant-chirped nanosecond pulses from an ultra-long nanotube mode-locked fiber laser.

We demonstrate that the giant chirp of coherent, nanosecond pulses generated in an 846 m long, all-normal dispersion, nanotube mode-locked fiber laser can be compensated using a chirped fiber Bragg grating compressor. Linear compression to 11 ps is reported, corresponding to an extreme compression factor of ∼100. Experimental results are supported by numerical modeling, which is also used to probe the limits of this technique. Our results unequivocally conclude that ultra-long cavity fiber lasers can support stable dissipative soliton attractors and highlight the design simplicity for pulse-energy scaling through cavity elongation.

Tunable Q-switched fiber laser based on saturable edge-state absorption in few-layer molybdenum disulfide (MoS2).

We fabricate a few-layer molybdenum disulfide (MoS2) polymer composite saturable absorber by liquid-phase exfoliation, and use this to passively Q-switch an ytterbium-doped fiber laser, tunable from 1030 to 1070 nm. Self-starting Q-switching generates 2.88 µs pulses at 74 kHz repetition rate, with over 100 nJ pulse energy. We propose a mechanism, based on edge states within the bandgap, responsible for the wideband nonlinear optical absorption exhibited by our few-layer MoS2 sample, despite operating at photon energies lower than the material bandgap.

Fiber-integrated 780 nm source for visible parametric generation.

We report the development of a fully fiber-integrated pulsed master oscillator power fibre amplifier (MOPFA) source at 780 nm, producing 3.5 W of average power with 410 ps pulses at a repetition rate of 50 MHz. The source consists of an intensity modulated 1560 nm laser diode amplified in an erbium fiber amplifier chain, followed by a fiber coupled periodically poled lithium niobate crystal module for frequency doubling. The source is then used for generating visible light through four-wave mixing in a length of highly nonlinear photonic crystal fiber: 105 mW at 668 nm and 95 mW at 662 nm are obtained, with pump to anti-Stokes conversion slope efficiencies exceeding 6% in both cases.

Stimulated Brillouin scattering of visible light in small-core photonic crystal fibers.

We characterize stimulated Brillouin scattering (SBS) of visible light in small-core photonic crystal fiber (PCF). Threshold powers under 532 nm excitation agree with established theory, in contrast to measured values up to five times greater than expected for Brillouin scattering of 1550 nm light. An isolated, single-peaked signal at a Stokes shift of 33.5 GHz is observed, distinct from the multi-peaked Stokes spectra expected when small-core PCF is pumped in the infrared. This wavelength-dependence of the Brillouin threshold, and the corresponding spectrum, are explained by the acousto-optic interactions in the fiber, governed by dimensionless length scales that relate the modal area to the core size, and the pump wavelength to PCF hole pitch. Our results suggest new opportunities for exploiting SBS of visible light in small-core PCFs.

Safety, pharmacokinetics, and pharmacodynamics of LBP-EC01, a CRISPR-Cas3-enhanced bacteriophage cocktail, in uncomplicated urinary tract infections due to Escherichia coli (ELIMINATE): the randomised, open-label, first part of a two-part phase 2 trial.

BACKGROUND: The rate of antibiotic resistance continues to grow, outpacing small-molecule-drug development efforts. Novel therapies are needed to combat this growing threat, particularly for the treatment of urinary tract infections (UTIs), which are one of the largest contributors to antibiotic use and associated antibiotic resistance. LBP-EC01 is a novel, genetically enhanced, six-bacteriophage cocktail developed by Locus Biosciences (Morrisville, NC, USA) to address UTIs caused by Escherichia coli, regardless of antibiotic resistance status. In this first part of the two-part phase 2 ELIMINATE trial, we aimed to define a dosing regimen of LBP-EC01 for the treatment of uncomplicated UTIs that could advance to the second, randomised, controlled, double-blinded portion of the study. METHODS: This first part of ELIMINATE is a randomised, uncontrolled, open-label, phase 2 trial that took place in six private clinical sites in the USA. Eligible participants were female by self-identification, aged between 18 years and 70 years, and had an uncomplicated UTI at the time of enrolment, as well as a history of at least one drug-resistant UTI caused by E coli within the 12 months before enrolment. Participants were initially randomised in a 1:1:1 ratio into three treatment groups, but this part of the trial was terminated on the recommendation of the safety review committee after a non-serious tolerability signal was observed based on systemic drug exposure. A protocol update was then implemented, comprised of three new treatment groups. Groups A to C were dosed with intraurethral 2 × 1012 plaque-forming units (PFU) of LBP-EC01 on days 1 and 2 by catheter, plus one of three intravenous doses daily on days 1-3 of LBP-EC01 (1 mL of 1 × 1010 PFU intravenous bolus in group A, 1 mL of 1 × 109 PFU intravenous bolus in group B, and a 2 h 1 × 1011 PFU intravenous infusion in 100 mL of sodium lactate solution in group C). In all groups, oral trimethoprim-sulfamethoxazole (TMP-SMX; 160 mg and 800 mg) was given twice daily on days 1-3. The primary outcome was the level of LBP-EC01 in urine and blood across the treatment period and over 48 h after the last dose and was assessed in patients in the intention-to-treat (ITT) population who received at least one dose of LBP-EC01 and had concentration-time data available throughout the days 1-3 dosing period (pharmacokinetic population). Safety, a secondary endpoint, was assessed in enrolled patients who received at least one dose of study drug (safety population). As exploratory pharmacodynamic endpoints, we assessed E coli levels in urine and clinical symptoms of UTI in patients with at least 1·0 × 105 colony-forming units per mL E coli in urine at baseline who took at least one dose of study drug and completed their day 10 test-of-cure assessment (pharmacodynamic-evaluable population). This trial is registered with ClinicalTrials.gov, NCT05488340, and is ongoing. FINDINGS: Between Aug 22, 2022, and Aug 28, 2023, 44 patients were screened for eligibility, and 39 were randomly assigned (ITT population). Initially, eight participants were assigned to the first three groups. After the protocol was updated, 31 participants were allocated into groups A (11 patients), B (ten patients), and C (ten patients). One patient in group C withdrew consent on day 2 for personal reasons, but as she had received the first dose of the study drug was included in the modified ITT population. Maximum urine drug concentrations were consistent across intraurethral dosing, with a maximum mean concentration of 6·3 × 108 PFU per mL (geometric mean 8·8 log10 PFU per mL and geometric SD [gSD] 0·3). Blood plasma level of bacteriophages was intravenous dose-dependent, with maximum mean concentrations of 4·0 × 103 (geometric mean 3·6 log10 PFU per mL [gSD 1·5]) in group A, 2·5 × 103 (3·4 log10 PFU per mL [1·7]) in group B, and 8·0 × 105 (5·9 log10 PFU per mL [1·4]) in group C. No serious adverse events were observed. 44 adverse events were reported across 18 (46%) of the 39 participants in the safety population, with more adverse events seen with higher intravenous doses. Three patients in groups 1 to 3 and one patient in group C, all of whom received 1 × 1011 LBP-EC01 intravenously, had non-serious tachycardia and afebrile chills after the second intravenous dose. A rapid reduction of E coli in urine was observed by 4 h after the first treatment and maintained at day 10 in all 16 evaluable patients; these individuals had complete resolution of UTI symptoms by day 10. INTERPRETATION: A regimen consisting of 2 days of intraurethral LBP-EC01 and 3 days of concurrent intravenous LBP-EC01 (1 × 1010 PFU) and oral TMP-SMX twice a day was well tolerated, with consistent pharmacokinetic profiles in urine and blood. LBP-EC01 and TMP-SMX dosing resulted in a rapid and durable reduction of E coli, with corresponding elimination of clinical symptoms in evaluable patients. LBP-EC01 holds promise in providing an alternative therapy for uncomplicated UTIs, with further testing of the group A dosing regimen planned in the controlled, double-blind, second part of ELIMINATE. FUNDING: Federal funds from the US Department of Health and Human Services, Administration for Strategic Preparedness and Response, and Biomedical Advanced Research and Development Authority (BARDA).

Characterization of nonlinear saturation and mode-locking potential of ionically-doped colored glass filter for short-pulse fiber lasers.

The nonlinear saturable absorption of an ionically-doped colored glass filter is measured directly using a Z-scan technique. For the first time, we demonstrate the potential of this material as a saturable asborber in fiber lasers. We achieve mode-locking of an ytterbium doped system. Mode-locking of cavities with all-positive and net-negative group velocity dispersion are demonstrated, achieving pulse durations of 60 ps and 4.1 ps, respectively. This inexpensive and optically robust material, with the potential for broadband operation, could surplant other saturable absorber devices in affordable mode-locked fiber lasers.