Index-Coupled Distributed-Feedback Semiconductor Quantum Cascade Lasers Fabricated Without Epitaxial Regrowth

Quantum cascade (QC) lasers and methods of fabricating such QC lasers are provided. The QC lasers incorporate a DFB grating without requiring the use of relying on epitaxial regrowth processes. The DFB gratings are formed as sidewall gratings along the lateral length of the QC active region, or the DFB gratings are formed atop the lateral length of the QC active region, and wherein the top DFB grating is planarized with a polymeric material

High-Power Single-Mode 2.65-micron InGaAsSb/AlInGaAsSb Diode Lasers

Central to the advancement of both satellite and in-situ science are improvements in continuous-wave and pulsed infrared laser systems coupled with integrated miniaturized optics and electronics, allowing for the use of powerful, single-mode light sources aboard both satellite and unmanned aerial vehicle platforms. There is a technological gap in supplying adequate laser sources to address the mid-infrared spectral window for spectroscopic characterization of important atmospheric gases. For high-power applications between 2 to 3 micron, commercial laser technologies are unsuitable because of limitations in output power. For instance, existing InP-based laser systems developed for fiber-based telecommunications cannot be extended to wavelengths longer than 2 micron. For emission wavelengths shorter than 3 micron, intersubband devices, such as infrared quantum cascade lasers, become inefficient due to band-offset limitations. To date, successfully demonstrated singlemode GaSb-based laser diodes emitting between 2 and 3 micron have employed lossy metal Bragg gratings for distributed- feedback coupling, which limits output power due to optical absorption. By optimizing both the quantum well design and the grating fabrication process, index-coupled distributed-feedback 2.65-micron lasers capable of emitting in excess of 25 mW at room temperature have been demonstrated. Specifically, lasers at 3,777/cm (2.65 micron) have been realized to interact with strong absorption lines of HDO and other isotopologues of H2O. With minor modifications of the optical cavity and quantum well designs, lasers can be fabricated at any wavelength within the 2-to-3-micron spectral window with similar performance. At the time of this reporting, lasers with this output power and wavelength accuracy are not commercially available. Monolithic ridge-waveguide GaSb lasers were fabricated that utilize secondorder lateral Bragg gratings to generate single-mode emission from InGaAsSb/ AlInGaAsSb multi-quantum well structures. The device fabrication utilizes etched index-coupled gratings in the top AlGaAsSb cladding of the laser chip along the ridge waveguide, whereas commercial lasers that emit close to this wavelength include loss-coupled metal gratings that limit the output power of the laser. Semiconductor-laser-based spectrometers can be used to replace gas sensors currently used in industry and government. With the availability of high-power laser sources at mid-infrared wavelengths, sensors can target strong fundamental gas absorption lines to maximize instrument sensitivity

Single-mode 2.65 µm InGaAsSb/AlInGaAsSb laterally coupled distributed-feedback diode lasers for atmospheric gas detection.

We demonstrate index-coupled distributed-feedback diode lasers at 2.65 µm that are capable of tuning across strong absorption lines of HDO and other isotopologues of H2O. The lasers employ InGaAsSb/AlInGaAsSb multi-quantum-well structures grown by molecular beam epitaxy on GaSb, and single-mode emission is generated using laterally coupled second-order Bragg gratings etched alongside narrow ridge waveguides. We verify near-critical coupling of the gratings by analyzing the modal characteristics of lasers of different length. With an emission facet anti-reflection coating, 2-mm-long lasers exhibit a typical current threshold of 150 mA at 20 °C and are capable of emitting more than 25 mW in a single longitudinal mode, which is significantly higher than the output power reported for loss-coupled distributed-feedback lasers operating at similar wavelengths

CW Performance of an InGaAs-GaAs-AlGaAs Laterally-Coupled Distributed Feedback (LC-DFB) Ridge Laser Diode

Single-mode distributed feedback (DFB) laser diodes typically require a two-step epitaxial growth or use of a corrugated substrate. We demonstrate InGaAs-GaAs-AlGaAs DFB lasers fabricated from a single epitaxial growth using lateral evanescent coupling of the optical field to a surface grating etehed along the sides of the ridge. A CW threshold current of 25 mA and external quantum efficiency of 0.48 mW/mA per facet were measured for a 1 mm cavity length device with anti-reflection coated facets. Single-mode output powers as high as 11 mW per facet at 935 nm wavelength were attained. A coupling coefficient of at least 5.8/cm was calculated from the subthreshold spectrum taking into account the 2% residual facet reflectivity

Comparative genomic analysis of the DUF71/COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage

Background: The availability of over 3000 published genome sequences has enabled the use of comparative genomic approaches to drive the biological function discovery process. Classically, one used to link gene with function by genetic or biochemical approaches, a lengthy process that often took years. Phylogenetic distribution profiles, physical clustering, gene fusion, co-expression profiles, structural information and other genomic or post-genomic derived associations can be now used to make very strong functional hypotheses. Here, we illustrate this shift with the analysis of the DUF71/COG2102 family, a subgroup of the PP-loop ATPase family. Results: The DUF71 family contains at least two subfamilies, one of which was predicted to be the missing diphthine-ammonia ligase (EC 6.3.1.14), Dph6. This enzyme catalyzes the last ATP-dependent step in the synthesis of diphthamide, a complex modification of Elongation Factor 2 that can be ADP-ribosylated by bacterial toxins. Dph6 orthologs are found in nearly all sequenced Archaea and Eucarya, as expected from the distribution of the diphthamide modification. The DUF71 family appears to have originated in the Archaea/Eucarya ancestor and to have been subsequently horizontally transferred to Bacteria. Bacterial DUF71 members likely acquired a different function because the diphthamide modification is absent in this Domain of Life. In-depth investigations suggest that some archaeal and bacterial DUF71 proteins participate in B12 salvage. Conclusions: This detailed analysis of the DUF71 family members provides an example of the power of integrated data-miming for solving important “missing genes” or “missing function” cases and illustrates the danger of functional annotation of protein families by homology alone. Reviewers’ names: This article was reviewed by Arcady Mushegian, Michael Galperin and L. Aravind

Reversing Blood Flows Act through klf2a to Ensure Normal Valvulogenesis in the Developing Heart

Heart valve anomalies are some of the most common congenital heart defects, yet neither the genetic nor the epigenetic forces guiding heart valve development are well understood. When functioning normally, mature heart valves prevent intracardiac retrograde blood flow; before valves develop, there is considerable regurgitation, resulting in reversing (or oscillatory) flows between the atrium and ventricle. As reversing flows are particularly strong stimuli to endothelial cells in culture, an attractive hypothesis is that heart valves form as a developmental response to retrograde blood flows through the maturing heart. Here, we exploit the relationship between oscillatory flow and heart rate to manipulate the amount of retrograde flow in the atrioventricular (AV) canal before and during valvulogenesis, and find that this leads to arrested valve growth. Using this manipulation, we determined that klf2a is normally expressed in the valve precursors in response to reversing flows, and is dramatically reduced by treatments that decrease such flows. Experimentally knocking down the expression of this shear-responsive gene with morpholine antisense oligonucleotides (MOs) results in dysfunctional valves. Thus, klf2a expression appears to be necessary for normal valve formation. This, together with its dependence on intracardiac hemodynamic forces, makes klf2a expression an early and reliable indicator of proper valve development. Together, these results demonstrate a critical role for reversing flows during valvulogenesis and show how relatively subtle perturbations of normal hemodynamic patterns can lead to both major alterations in gene expression and severe valve dysgenesis

The Mechanism of Substrate Inhibition in Human Indoleamine 2,3-Dioxygenase

Indoleamine 2,3-dioxygenase catalyzes the O(2)-dependent oxidation of L-tryptophan (L-Trp) to N-formylkynurenine (NFK) as part of the kynurenine pathway. Inhibition of enzyme activity at high L-Trp concentrations was first noted more than 30 years ago, but the mechanism of inhibition has not been established. Using a combination of kinetic and reduction potential measurements, we present evidence showing that inhibition of enzyme activity in human indoleamine 2,3-dioxygenase (hIDO) and a number of site-directed variants during turnover with L-tryptophan (L-Trp) can be accounted for by the sequential, ordered binding of O(2) and L-Trp. Analysis of the data shows that at low concentrations of L-Trp, O(2) binds first followed by the binding of L-Trp; at higher concentrations of L-Trp, the order of binding is reversed. In addition, we show that the heme reduction potential (E(m)(0)) has a regulatory role in controlling the overall rate of catalysis (and hence the extent of inhibition) because there is a quantifiable correlation between E(m)(0) (that increases in the presence of L-Trp) and the rate constant for O(2) binding. This means that the initial formation of ferric superoxide (Fe(3+)-O(2)(•-)) from Fe(2+)-O(2) becomes thermodynamically less favorable as substrate binds, and we propose that it is the slowing down of this oxidation step at higher concentrations of substrate that is the origin of the inhibition. In contrast, we show that regeneration of the ferrous enzyme (and formation of NFK) in the final step of the mechanism, which formally requires reduction of the heme, is facilitated by the higher reduction potential in the substrate-bound enzyme and the two constants (k(cat) and E(m)(0)) are shown also to be correlated. Thus, the overall catalytic activity is balanced between the equal and opposite dependencies of the initial and final steps of the mechanism on the heme reduction potential. This tuning of the reduction potential provides a simple mechanism for regulation of the reactivity, which may be used more widely across this family of enzymes

Construction and in vivo assembly of a catalytically proficient and hyperthermostable de novo enzyme

Although catalytic mechanisms in natural enzymes are well understood, achieving the diverse palette of reaction chemistries in re-engineered native proteins has proved challenging. Wholesale modification of natural enzymes is potentially compromised by their intrinsic complexity, which often obscures the underlying principles governing biocatalytic efficiency. The maquette approach can circumvent this complexity by combining a robust de novo designed chassis with a design process that avoids atomistic mimicry of natural proteins. Here, we apply this method to the construction of a highly efficient, promiscuous, and thermostable artificial enzyme that catalyzes a diverse array of substrate oxidations coupled to the reduction of H2O2. The maquette exhibits kinetics that match and even surpass those of certain natural peroxidases, retains its activity at elevated temperature and in the presence of organic solvents, and provides a simple platform for interrogating catalytic intermediates common to natural heme-containing enzymes

The TINCR ubiquitin-like microprotein is a tumor suppressor in squamous cell carcinoma

The TINCR (Terminal differentiation-Induced Non-Coding RNA) gene is selectively expressed in epithelium tissues and is involved in the control of human epidermal differentiation and wound healing. Despite its initial report as a long non-coding RNA, the TINCR locus codes for a highly conserved ubiquitin-like microprotein associated with keratinocyte differentiation. Here we report the identification of TINCR as a tumor suppressor in squamous cell carcinoma (SCC). TINCR is upregulated by UV-induced DNA damage in a TP53-dependent manner in human keratinocytes. Decreased TINCR protein expression is prevalently found in skin and head and neck squamous cell tumors and TINCR expression suppresses the growth of SCC cells in vitro and in vivo. Consistently, Tincr knockout mice show accelerated tumor development following UVB skin carcinogenesis and increased penetrance of invasive SCCs. Finally, genetic analyses identify loss-of-function mutations and deletions encompassing the TINCR gene in SCC clinical samples supporting a tumor suppressor role in human cancer. Altogether, these results demonstrate a role for TINCR as protein coding tumor suppressor gene recurrently lost in squamous cell carcinomas.This work was supported by NIH grants P30 CA013696 (Confocal and Specialized Microscopy Shared Resource, Proteomics Shared Resource, Molecular Pathology Shared Resource, Genomics Shared Resource, Herbert Irving Comprehensive Cancer Center), R01 GM102491 (A.S.), K01 CA249038 (T.F.M.), P30 AR069632 (epiCURE SCIM and SIND Core Facilities) and R35 CA210065 (A.A.F.); Dr. Frederick Paulsen Chair/Ferring Pharmaceuticals (A.S.); Plan Nacional de I + D + I/ISCIII grants PI16/00280 and PI19/00560 (J.M.G.-P.), and PI18/01527 (M.F.F. and A.F.F.); CIBERONC grant CB16/12/00390 (J.P.R.), and the FEDER Funding Program from the European Union. Crystallization screening at the National Crystallization Center at HWI was supported through NIH grant R24GM141256. This work used the NE-CAT 24-ID-E beamline (GM124165) and an Eiger detector (OD021527) at the APS (DE-AC02-06CH11357). LMP was supported by a Leukemia and Lymphoma Society Career Development fellowship (grant #5461-18). J.A.B. was the Candy and William Raveis Fellow of the Damon Runyon-Sohn Foundation Pediatric Cancer Fellowship Award (grant no. DRSG-31-19) and supported by the National Cancer Institute of the National Institutes of Health (award no. K99CA267168). R.G.-D. is a recipient of a Severo Ochoa predoctoral fellowship from the Principado de Asturias (grant # BP19-063).Peer reviewe