Interactions of ruthenium(II) polypyridyl complexes with human telomeric DNA.

Eight [Ru(bpy)2L]2+ and three [Ru(phen)2L]2+complexes (where bpy = 2,2'-bipyridine and phen = 1,10-phenanthroline are ancillary ligands, and L = a polypyridyl experimental ligand) were investigated for their G-quadruplex binding abilities. Fluorescence resonance energy transfer melting assays were used to screen these complexes for their ability to selectively stabilize human telomeric DNA variant, Tel22. The best G-quadruplex stabilizers were further characterized for their binding properties (binding constant and stoichiometry) using UV-vis, fluorescence spectroscopy, and mass spectrometry. The ligands' ability to alter the structure of Tel22 was determined via circular dichroism and PAGE studies. We identified me2allox as the experimental ligand capable of conferring excellent stabilizing ability and good selectivity to polypyridyl Ru(II) complexes. Replacing bpy by phen did not significantly impact interactions with Tel22, suggesting that binding involves mostly the experimental ligand. However, using a particular ancillary ligand can help fine-tune G-quadruplex-binding properties of Ru(II) complexes. Finally, the fluorescence "light switch" behavior of all Ru(II) complexes in the presence of Tel22 G-quadruplex was explored. All Ru(II) complexes displayed "light switch" properties, especially [Ru(bpy)2(diamino)]2+, [Ru(bpy)2(dppz)]2+, and [Ru(bpy)2(aap)]2+. Current work sheds light on how Ru(II) polypyridyl complexes interact with human telomeric DNA with possible application in cancer therapy or G-quadruplex sensing.

Asymmetric Carbohydroxylation of Alkenes Using Photoenzymatic Catalysis.

Alkene difunctionalizations enable the synthesis of structurally elaborated products from simple and ubiquitous starting materials in a single chemical step. Carbohydroxylations of olefins represent a family of reactivity that furnish structurally complex alcohols. While examples of this type of three-component coupling have been reported, catalytic asymmetric examples remain elusive. Here, we report an enzyme-catalyzed asymmetric carbohydroxylation of alkenes catalyzed by flavin-dependent "ene"-reductases to produce enantioenriched tertiary alcohols. Seven rounds of protein engineering reshape the enzyme's active site to increase activity and enantioselectivity. Mechanistic studies suggest that C-O bond formation occurs via a 5-endo-trig cyclization with the pendant ketone to afford an α-oxy radical which is oxidized and hydrolyzed to form the product. This work demonstrates photoenzymatic reactions involving "ene"-reductases can terminate radicals via mechanisms other than hydrogen atom transfer, expanding their utility in chemical synthesis.

Photobiocatalytic Strategies for Organic Synthesis.

Biocatalysis has revolutionized chemical synthesis, providing sustainable methods for preparing various organic molecules. In enzyme-mediated organic synthesis, most reactions involve molecules operating from their ground states. Over the past 25 years, there has been an increased interest in enzymatic processes that utilize electronically excited states accessed through photoexcitation. These photobiocatalytic processes involve a diverse array of reaction mechanisms that are complementary to one another. This comprehensive review will describe the state-of-the-art strategies in photobiocatalysis for organic synthesis until December 2022. Apart from reviewing the relevant literature, a central goal of this review is to delineate the mechanistic differences between the general strategies employed in the field. We will organize this review based on the relationship between the photochemical step and the enzymatic transformations. The review will include mechanistic studies, substrate scopes, and protein optimization strategies. By clearly defining mechanistically-distinct strategies in photobiocatalytic chemistry, we hope to illuminate future synthetic opportunities in the area.

Anatomical and functional outcomes of short-term DensironXTRA heavy silicone oil for rhegmatogenous retinal detachments: a comparative case series.

To assess the safety and efficacy of short-term DensironXTRA tamponade for repair of complicated rhegmatogenous retinal detachments (RRD). This is a retrospective consecutive case series of patients undergoing pars plana vitrectomy (PPV) with intravitreal DensironXTRA and a comparator group with gas (sulfur hexafluoride (SF6) or perfluoropropane (C3F8)) tamponades by a single surgeon between January 2017 and November 2020 at a tertiary care centre. A total of 121 eyes with DensironXTRA and 81 comparator eyes with a gas tamponade were included. The DensironXTRA group had a significantly higher number of cases with inferior breaks (82% vs. 48%; p < 0.0001) and a history of previous PPV for RRD (64% vs. 12%; p < 0.0001). DensironXTRA was removed after a median period of 70 (IQR: 48.5-105.5) days. There was similar anatomical success in both the comparator gas tamponade and DensironXTRA groups (98.8% vs. 97.5%, p = 0.6506). Although both groups experienced a significant improvement in visual acuity, this change was significantly higher in the comparator gas tamponade group versus DensironXTRA group (p = 0.0017). There was no significant change in IOP in the DensironXTRA group (mean difference - 0.7; 95% CI - 1.753 to 0.331, p = 0.1785). The rates of complications were low and not significantly different between the two groups. There was no evidence for central macular thinning with DensironXTRA compared to the contralateral eye without RRD as well as with DensironXTRA in situ versus after its removal. DensironXTRA is a promising short-term tamponade agent with good anatomical and functional outcomes and low rates of complications for the repair of complicated RRDs.

Electrically pumped quantum-dot lasers grown on 300 mm patterned Si photonic wafers.

Monolithic integration of quantum dot (QD) gain materials onto Si photonic platforms via direct epitaxial growth is a promising solution for on-chip light sources. Recent developments have demonstrated superior device reliability in blanket hetero-epitaxy of III-V devices on Si at elevated temperatures. Yet, thick, defect management epi designs prevent vertical light coupling from the gain region to the Si-on-Insulator waveguides. Here, we demonstrate the first electrically pumped QD lasers grown by molecular beam epitaxy on a 300 mm patterned (001) Si wafer with a butt-coupled configuration. Unique growth and fabrication challenges imposed by the template architecture have been resolved, contributing to continuous wave lasing to 60 °C and a maximum double-side output power of 126.6 mW at 20 °C with a double-side wall-plug efficiency of 8.6%. The potential for robust on-chip laser operation and efficient low-loss light coupling to Si photonic circuits makes this heteroepitaxial integration platform on Si promising for scalable and low-cost mass production.

Pediatric Musculoskeletal Radiographs: Anatomy and Fractures Prone to Diagnostic Error Among Emergency Physicians.

BACKGROUND: Pediatric musculoskeletal (pMSK) radiograph interpretations are common, but the specific radiograph features at risk of incorrect diagnosis are relatively unknown. OBJECTIVE: We determined the radiograph factors that resulted in diagnostic interpretation challenges for emergency physicians (EPs) reviewing pMSK radiographs. METHODS: EPs interpreted 1850 pMSK radiographs via a web-based platform and we derived interpretation difficulty scores for each radiograph in 13 body regions using one-parameter item response theory. We compared the difficulty scores by presence or absence of a fracture and, where applicable, by fracture location and morphology; significance was adjusted for multiple comparisons. An expert panel reviewed the 65 most commonly misdiagnosed fracture-negative radiographs to identify imaging features mistaken for fractures. RESULTS: We included data from 244 EPs, which resulted in 185,653 unique interpretations. For elbow, forearm, wrist, femur, knee, and tibia-fibula radiographs, those without a fracture had higher interpretation difficulty scores relative to those with a fracture; the opposite was true for the hand, pelvis, foot, and ankle radiographs (p < 0.004 for all comparisons). The descriptive review demonstrated that specific normal anatomy, overlapping bones, and external artefact from muscle or skin folds were often mistaken for fractures. There was a significant difference in difficulty score by anatomic locations of the fracture in the elbow, pelvis, and ankle (p < 0.004 for all comparisons). Ankle and elbow growth plate, fibular avulsion, and humerus condylar fractures were more difficult to diagnose than other fracture patterns (p < 0.004 for all comparisons). CONCLUSIONS: We identified actionable learning opportunities in pMSK radiograph interpretation for EPs.

Learning Pediatric Point-of-Care Ultrasound: How Many Cases Does Mastery of Image Interpretation Take?

OBJECTIVES: Using an education and assessment tool, we examined the number of cases necessary to achieve a performance benchmark in image interpretation of pediatric soft tissue, cardiac, lung, and focused assessment with sonography for trauma (FAST) point-of-care ultrasound (POCUS) applications. We also determined interpretation difficulty scores to derive which cases provided the greatest diagnostic challenges. METHODS: Pediatric emergency physicians participated in web-based pediatric POCUS courses sponsored by their institution as a credentialing priority. Participants deliberately practiced cases until they achieved diagnostic interpretation scores of combined 90% accuracy, sensitivity, and specificity. RESULTS: Of the 463 who enrolled, 379 (81.9%) completed cases. The median (interquartile range) number of cases required to achieve the performance benchmark for soft tissue was 94 (68-128); cardiac, 128 (86-201); lung, 87 (25-118); and FAST, 93 (68-133) (P < 0001). Specifically, cases completed to achieve benchmark were higher for cardiac relative to other applications (P < 0.0001 for all comparisons). In soft tissue cases, a foreign body was more difficult to diagnose than cobblestoning and hypoechoic collections (P = 0.036). Poor cardiac function and abnormal ventricles were more difficult to interpret with accuracy than normal (P < 0.0001) or pericardial effusion cases (P = 0.01). The absence of lung sliding was significantly more difficult to interpret than normal lung cases (P = 0.028). The interpretation difficulty of various FAST imaging findings was not significantly different. CONCLUSIONS: There was a significant variation in number of cases required to reach a performance benchmark. We also identified the specific applications and imaging findings that demonstrated the greatest diagnostic challenges. These data may inform future credentialing guidelines and POCUS learning interventions.

A Target Population Derived Method for Developing a Competency Standard in Radiograph Interpretation.

CONSTRUCT: For assessing the skill of visual diagnosis such as radiograph interpretation, competency standards are often developed in an ad hoc method, with a poorly delineated connection to the target clinical population. BACKGROUND: Commonly used methods to assess for competency in radiograph interpretation are subjective and potentially biased due to a small sample size of cases, subjective evaluations, or include an expert-generated case-mix versus a representative sample from the clinical field. Further, while digital platforms are available to assess radiograph interpretation skill against an objective standard, they have not adopted a data-driven competency standard which informs educators and the public that a physician has achieved adequate mastery to enter practice where they will be making high-stakes clinical decisions. APPROACH: Operating on a purposeful sample of radiographs drawn from the clinical domain, we adapted the Ebel Method, an established standard setting method, to ascertain a defensible, clinically relevant mastery learning competency standard for the skill of radiograph interpretation as a model for deriving competency thresholds in visual diagnosis. Using a previously established digital platform, emergency physicians interpreted pediatric musculoskeletal extremity radiographs. Using one-parameter item response theory, these data were used to categorize radiographs by interpretation difficulty terciles (i.e. easy, intermediate, hard). A panel of emergency physicians, orthopedic surgeons, and plastic surgeons rated each radiograph with respect to clinical significance (low, medium, high). These data were then used to create a three-by-three matrix where radiographic diagnoses were categorized by interpretation difficulty and significance. Subsequently, a multidisciplinary panel that included medical and parent stakeholders determined acceptable accuracy for each of the nine cells. An overall competency standard was derived from the weighted sum. Finally, to examine consequences of implementing this standard, we reported on the types of diagnostic errors that may occur by adhering to the derived competency standard. FINDINGS: To determine radiograph interpretation difficulty scores, 244 emergency physicians interpreted 1,835 pediatric musculoskeletal extremity radiographs. Analyses of these data demonstrated that the median interpretation difficulty rating of the radiographs was -1.8 logits (IQR -4.1, 3.2), with a significant difference of difficulty across body regions (p < 0.0001). Physician review classified the radiographs as 1,055 (57.8%) as low, 424 (23.1%) medium or 356 (19.1%) high clinical significance. The multidisciplinary panel suggested a range of acceptable scores between cells in the three-by-three table of 76% to 95% and the sum of equal-weighted scores resulted in an overall performance-based competency score of 85.5% accuracy. Of the 14.5% diagnostic interpretation errors that may occur at the bedside if this competency standard were implemented, 9.8% would be in radiographs of low-clinical significance, while 2.5% and 2.3% would be in radiographs of medium or high clinical significance, respectively. CONCLUSION(S): This study's novel integration of radiograph selection and a standard setting method could be used to empirically drive evidence-based competency standard for radiograph interpretation and can serve as a model for deriving competency thresholds for clinical tasks emphasizing visual diagnosis.

Photoenzymatic Synthesis of α-Tertiary Amines by Engineered Flavin-Dependent "Ene"-Reductases.

α-Tertiary amines are a common motif in pharmaceutically important molecules but are challenging to prepare using asymmetric catalysis. Here, we demonstrate engineered flavin-dependent 'ene'-reductases (EREDs) can catalyze radical additions into oximes to prepare this motif. Two different EREDs were evolved into competent catalysts for this transformation with high levels of stereoselectivity. Mechanistic studies indicate that the oxime contributes to the enzyme templated charge-transfer complex formed between the substrate and cofactor. These products can be further derivatized to prepare a variety of motifs, highlighting the versatility of ERED photoenzymatic catalysis for organic synthesis.

NusG controls transcription pausing and RNA polymerase translocation throughout the Bacillus subtilis genome.

Transcription is punctuated by RNA polymerase (RNAP) pausing. These pauses provide time for diverse regulatory events that can modulate gene expression. Transcription elongation factors dramatically affect RNAP pausing in vitro, but the genome-wide role of such factors on pausing has not been examined. Using native elongating transcript sequencing followed by RNase digestion (RNET-seq), we analyzed RNAP pausing in Bacillus subtilis genome-wide and identified an extensive role of NusG in pausing. This universally conserved transcription elongation factor is known as Spt5 in archaeal and eukaryotic organisms. B. subtilis NusG shifts RNAP to the posttranslocation register and induces pausing at 1,600 sites containing a consensus TTNTTT motif in the nontemplate DNA strand within the paused transcription bubble. The TTNTTT motif is necessary but not sufficient for NusG-dependent pausing. Approximately one-fourth of these pause sites were localized to untranslated regions and could participate in posttranscription initiation control of gene expression as was previously shown for tlrB and the trpEDCFBA operon. Most of the remaining pause sites were identified in protein-coding sequences. NusG-dependent pausing was confirmed for all 10 pause sites that we tested in vitro. Putative pause hairpins were identified for 225 of the 342 strongest NusG-dependent pause sites, and some of these hairpins were shown to function in vitro. NusG-dependent pausing in the ribD riboswitch provides time for cotranscriptional binding of flavin mononucleotide, which decreases the concentration required for termination upstream of the ribD coding sequence. Our phylogenetic analysis implicates NusG-dependent pausing as a widespread mechanism in bacteria.

Optimization of photoluminescence from W centers in a silicon-on-insulator.

W centers are trigonal defects generated by self-ion implantation in silicon that exhibit photoluminescence at 1.218 µm. We have shown previously that they can be used in waveguide-integrated all-silicon light-emitting diodes (LEDs). Here we optimize the implant energy, fluence and anneal conditions to maximize the photoluminescence intensity for W centers implanted in silicon-on-insulator, a substrate suitable for waveguide-integrated devices. After optimization, we observe near two orders of magnitude improvement in photoluminescence intensity relative to the conditions with the stopping range of the implanted ions at the center of the silicon device layer. The previously demonstrated waveguide-integrated LED used implant conditions with the stopping range at the center of this layer. We further show that such light sources can be manufactured at the 300-mm scale by demonstrating photoluminescence of similar intensity from 300 mm silicon-on-insulator wafers. The luminescence uniformity across the entire wafer is within the measurement error.

The Loss of ATRX Increases Susceptibility to Pancreatic Injury and Oncogenic KRAS in Female But Not Male Mice.

Background: Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer death in North America, accounting for >30,000 deaths annually. Although somatic activating mutations in KRAS appear in 97% of PDAC patients, additional factors are required to initiate PDAC. Because mutations in genes encoding chromatin remodelling proteins have been implicated in KRAS-mediated PDAC, we investigated whether loss of chromatin remodeler ɑ-thalassemia, mental-retardation, X-linked (ATRX) affects oncogenic KRAS's ability to promote PDAC. ATRX affects DNA replication, repair, and gene expression and is implicated in other cancers including glioblastomas and pancreatic neuroendocrine tumors. The hypothesis was that deletion of Atrx in pancreatic acinar cells will increase susceptibility to injury and oncogenic KRAS. Methods: Mice allowing conditional loss of Atrx within pancreatic acinar cells were examined after induction of recurrent cerulein-induced pancreatitis or oncogenic KRAS (KRASG12D ). Histologic, biochemical, and molecular analysis examined pancreatic pathologies up to 2 months after induction of Atrx deletion. Results: Mice lacking Atrx showed more progressive damage, inflammation, and acinar-to-duct cell metaplasia in response to injury relative to wild-type mice. In combination with KRASG12D, Atrx-deficient acinar cells showed increased fibrosis, inflammation, progression to acinar-to-duct cell metaplasia, and pre-cancerous lesions relative to mice expressing only KRASG12D. This sensitivity appears only in female mice, mimicking a significant prevalence of ATRX mutations in human female PDAC patients. Conclusions: Our results indicate the absence of ATRX increases sensitivity to injury and oncogenic KRAS only in female mice. This is an instance of a sex-specific mutation that enhances oncogenic KRAS's ability to promote pancreatic intraepithelial lesion formation.

Gαq and Phospholipase Cß signaling regulate nociceptor sensitivity in Drosophila melanogaster larvae.

Drosophila melanogaster larvae detect noxious thermal and mechanical stimuli in their environment using polymodal nociceptor neurons whose dendrites tile the larval body wall. Activation of these nociceptors by potentially tissue-damaging stimuli elicits a stereotyped escape locomotion response. The cellular and molecular mechanisms that regulate nociceptor function are increasingly well understood, but gaps remain in our knowledge of the broad mechanisms that control nociceptor sensitivity. In this study, we use cell-specific knockdown and overexpression to show that nociceptor sensitivity to noxious thermal and mechanical stimuli is correlated with levels of Gαq and phospholipase Cß signaling. Genetic manipulation of these signaling mechanisms does not result in changes in nociceptor morphology, suggesting that changes in nociceptor function do not arise from changes in nociceptor development, but instead from changes in nociceptor activity. These results demonstrate roles for Gαq and phospholipase Cß signaling in facilitating the basal sensitivity of the larval nociceptors to noxious thermal and mechanical stimuli and suggest future studies to investigate how these signaling mechanisms may participate in neuromodulation of sensory function.

RNA-DNA and DNA-DNA base-pairing at the upstream edge of the transcription bubble regulate translocation of RNA polymerase and transcription rate.

Translocation of RNA polymerase (RNAP) along DNA may be rate-limiting for transcription elongation. The Brownian ratchet model posits that RNAP rapidly translocates back and forth until the post-translocated state is stabilized by NTP binding. An alternative model suggests that RNAP translocation is slow and poorly reversible. To distinguish between these two models, we take advantage of an observation that pyrophosphorolysis rates directly correlate with the abundance of the pre-translocated fraction. Pyrophosphorolysis by RNAP stabilized in the pre-translocated state by bacteriophage HK022 protein Nun was used as a reference point to determine the pre-translocated fraction in the absence of Nun. The stalled RNAP preferentially occupies the post-translocated state. The forward translocation rate depends, among other factors, on melting of the RNA-DNA base pair at the upstream edge of the transcription bubble. DNA-DNA base pairing immediately upstream from the RNA-DNA hybrid stabilizes the post-translocated state. This mechanism is conserved between E. coli RNAP and S. cerevisiae RNA polymerase II and is partially dependent on the lid domain of the catalytic subunit. Thus, the RNA-DNA hybrid and DNA reannealing at the upstream edge of the transcription bubble emerge as targets for regulation of the transcription elongation rate.

Neuregulin-1 is a chemoattractant and chemokinetic molecule for trunk neural crest cells.

BACKGROUND: Trunk neural crest cells migrate rapidly along characteristic pathways within the developing vertebrate embryo. Proper trunk neural crest cell migration is necessary for the morphogenesis of much of the peripheral nervous system, melanocytes, and the adrenal medulla. Numerous molecules help guide trunk neural crest cell migration throughout the early embryo. RESULTS: The trophic factor NRG1 is a chemoattractant through in vitro chemotaxis assays and in vivo silencing via a DN-erbB receptor. Interestingly, we also observed changes in migratory responses consistent with a chemokinetic effect of NRG1 in trunk neural crest velocity. CONCLUSIONS: NRG1 is a trunk neural crest cell chemoattractant and chemokinetic molecule. Developmental Dynamics 247:888-902, 2018.. © 2018 Wiley Periodicals, Inc.

N-methylmesoporphyrin IX fluorescence as a reporter of strand orientation in guanine quadruplexes.

Guanine quadruplexes (GQ) are four-stranded DNA structures formed by guanine-rich DNA sequences. The formation of GQs inhibits cancer cell growth, although the detection of GQs in vivo has proven difficult, in part because of their structural diversity. The development of GQ-selective fluorescent reporters would enhance our ability to quantify the number and location of GQs, ultimately advancing biological studies of quadruplex relevance and function. N-methylmesoporphyrin IX (NMM) interacts selectively with parallel-stranded GQs; in addition, its fluorescence is sensitive to the presence of DNA, making this ligand a possible candidate for a quadruplex probe. In the present study, we investigated the effect of DNA secondary structure on NMM fluorescence. We found that NMM fluorescence increases by about 60-fold in the presence of parallel-stranded GQs and by about 40-fold in the presence of hybrid GQs. Antiparallel GQs lead to lower than 10-fold increases in NMM fluorescence. Single-stranded DNA, duplex, or i-motif, induce no change in NMM fluorescence. We conclude that NMM shows promise as a 'turn-on' fluorescent probe for detecting quadruplex structures, as well as for differentiating them on the basis of strand orientation.