Differential Substrate Sensing in Terpene Synthases from Plants and Microorganisms: Insight from Structural, Bioinformatic, and EnzyDock Analyses

Terpene synthases (TPSs) catalyze the first step in the formation of terpenoids, which comprise the largest class of natural products in nature. TPSs employ a family of universal natural substrates, composed of isoprenoid units bound to a diphosphate moiety. The intricate structures generated by TPSs are the result of substrate binding and folding in the active site, enzyme-controlled carbocation reaction cascades, and final reaction quenching. A key unaddressed question in class I TPSs is the asymmetric nature of the diphosphate-(Mg2+)3 cluster, which forms a critical part of the active site. In this asymmetric ion cluster, two diphosphate oxygen atoms protrude into the active site pocket. The substrate hydrocarbon tail, which is eventually molded into terpenes, can bind to either of these oxygen atoms, yet to which is unknown. Herein, we employ structural, bioinformatics, and EnzyDock docking tools to address this enigma. We bring initial data suggesting that this difference is rooted in evolutionary differences between TPSs. We hypothesize that this alteration in binding, and subsequent chemistry, is due to TPSs originating from plants or microorganisms. We further suggest that this difference can cast light on the frequent observation that the chiral products or intermediates of plant and bacterial terpene synthases represent opposite enantiomers.

Milestones in the natural course of the onset of e-cigarette dependence among adolescents and young adults: Retrospective study

INTRODUCTION

There is considerable controversy about the development of dependence among e-cigarette users. This study describes the average amount of time using e-cigarettes before dependence milestones emerge and the differences in developing dependence between e-cigarette users who smoke cigarettes compared to those who do not.

METHODS

Adolescents and young adults aged 16-25 living in Canada were recruited into an online survey in 2021. Current (past-month) e-cigarette users completed 15 items assessing dependence from the Penn-State Electronic Cigarette Dependence Index and the E-cigarette Dependence Scale for a total of 12 behavioural (e.g., difficulty refraining from vaping) and 3 frequency (e.g., using e-cigarette daily, weekly, or monthly) indicators of dependence milestones. Number of years after e-cigarette onset at which the cumulative probability of attaining each milestone was 25 % was computed.

RESULTS

Among 1205 participants, most (80.6 %) were female, 73.7 % were Caucasian, and 49.7 % resided in Ontario. Ten of the 12 e-cigarette use milestones were attained by 25 % of respondents 2 years after starting vaping except for daily cigarette use (2.5 years after onset) and waking at night to vape (5.6 years after onset). Within the entire study population, frequency milestones (weekly, monthly, daily e-cigarette use) were attained faster by ever-smokers (hazard ratio compared to attainment by never-smokers: 1.12, 1.21, and 1.28 respectively), whereas for at least monthly users, behavioural milestones were attained faster by never-smokers.

DISCUSSION

Many current e-cigarette users developed symptoms of e-cigarette dependence between two and five years since onset. Never smokers may be at higher risk of becoming e-cigarette dependent since they attained e-cigarette dependence milestones faster than smokers.

Copper coordination states affect the flexibility of copper Metallochaperone Atox1: Insights from molecular dynamics simulations

Copper is an essential element in nature but in excess, it is toxic to the living cell. The human metallochaperone Atox1 participates in copper homeostasis and is responsible for copper transmission. In a previous multiscale simulation study, we noticed a change in the coordination state of the Cu(I) ion, from 4 bound cysteine residues to 3, in agreement with earlier studies. Here, we perform and analyze classical molecular dynamic simulations of various coordination states: 2, 3, and 4. The main observation is an increase in protein flexibility as a result of a decrease in the coordination state. In addition, we identified several populated conformations that correlate well with double electron-electron resonance distance distributions or an X-ray structure of Cu(I)-bound Atox1. We suggest that the increased flexibility might benefit the process of ion transmission between interacting proteins. Further experiments can scrutinize this hypothesis and shed additional light on the mechanism of action of Atox1.

Cooperative Intrinsic Basicity and Hydrogen Bonding Render SmI2 More Azaphilic than Oxophilic

It has been recently shown that SmI₂ is more azaphilic than oxophilic. Density functional theory calculations reveal that coordination of 1-3 molecules of ethylenediamine is more exothermic by up to 10 kcal/mol than coordination of the corresponding number of ethylene glycol molecules. Taking into account also hydrogen bonds between ligands and tetrahydrofuran doubles this preference. The intrinsic affinity parallels the order of basicity. The cooperativity with the hydrogen bonding makes SmI₂ more azaphilic than oxophilic.

Are intravitreal injections essential during the COVID-19 pandemic? Global preferred practice patterns and practical recommendations

Tertiary outpatient ophthalmology clinics are high-risk environments for COVID-19 transmission, especially retina clinics, where regular follow-up is needed for elderly patients with multiple comorbidities. Intravitreal injection therapy (IVT) for chronic macular diseases, is one of the most common procedures performed, associated with a significant burden of care because of the vigorous treatment regimen associated with multiple investigations. While minimizing the risk of COVID-19 infection transmission is a priority, this must be balanced against the continued provision of sight-saving ophthalmic care to patients at risk of permanent vision loss. This review aims to give evidence-based guidelines on managing IVT during the COVID-19 pandemic in common macular diseases such as age-related macular degeneration, diabetic macula edema and retinal vascular disease and to report on how the COVID-19 pandemic has affected IVT practices worldwide.

To illustrate some real-world examples, 18 participants in the International Retina Collaborative, from 15 countries and across four continents, were surveyed regarding pre- and during- COVID-19 pandemic IVT practices in tertiary ophthalmic centers. The majority of centers reported a reduction in the number of appointments to reduce the risk of the spread of COVID-19 with varying changes to their IVT regimen to treat various macula diseases. Due to the constantly evolving nature of the COVID-19 pandemic, and the uncertainty about the normal resumption of health services, we suggest that new solutions for eye healthcare provision, like telemedicine, may be adopted in the future when we consider new long-term adaptations required to cope with the COVID-19 pandemic.

Two-color Kerr microscopy of two-dimensional materials with sub-picosecond time resolution

We present a two-color Kerr microscopy system based on two electronically synchronized erbium-fiber laser oscillators with independently tunable emission energies spanning most of the visible spectrum. Combining a spatial resolution below 2 μm and sub-ps time resolution with high sensitivity and cryogenic sample temperatures, it is ideally suited for studying spin and valley dynamics in a wide range of two-dimensional materials. We illustrate its capabilities by studying a monolayer of the common semiconducting transition metal disulfide MoS₂.

Molecular Dynamics Simulations of the Apo and Holo States of the Copper Binding Protein CueR Reveal Principal Bending and Twisting Motions

Copper is essential for proper functioning of cells but is dangerous in unregulated concentrations. One of the members in the bacterial system responsible for facilitating copper homeostasis is the copper efflux regulator (CueR) protein. Upon copper binding, CueR induces transcription of additional copper homeostasis proteins via a cascade of events. There are some available crystal structures of CueR, in the holo (copper-bound), active (copper- and DNA-bound), and repressed (only DNA-bound) states, and these structures suggest that transcription initiation involves a distortion in the promoter DNA strand. In this work, we study the dynamic behavior of the protein, using molecular dynamics simulations, and compare with available electron paramagnetic resonance measurements for validation. We develop simple force-field parameters to describe the copper-binding motif, thus enabling the use of simplified, classical physics equations. This enabled us to access reasonable simulation times that illustrate global motions of the protein. Both in the holo and apo states of CueR, we observed large-scale helical bending motions that could be involved in the bending of a bound DNA molecule so that transcription activation can take place. Additionally, copper binding might afford increased rigidification of the active state via helix α6.

Benchmarking the Ability of Common Docking Programs to Correctly Reproduce and Score Binding Modes in SARS-CoV-2 Protease Mpro

The coronavirus SARS-CoV-2 main protease, Mpro, is conserved among coronaviruses with no human homolog and has therefore attracted significant attention as an enzyme drug target for COVID-19. The number of studies targeting Mpro for in silico screening has grown rapidly, and it would be of great interest to know in advance how well docking methods can reproduce the correct ligand binding modes and rank these correctly. Clearly, current attempts at designing drugs targeting Mpro with the aid of computational docking would benefit from a priori knowledge of the ability of docking programs to predict correct binding modes and score these correctly. In the current work, we tested the ability of several leading docking programs, namely, Glide, DOCK, AutoDock, AutoDock Vina, FRED, and EnzyDock, to correctly identify and score the binding mode of Mpro ligands in 193 crystal structures. None of the codes were able to correctly identify the crystal structure binding mode (lowest energy pose with root-mean-square deviation < 2 Å) in more than 26% of the cases for noncovalently bound ligands (Glide: top performer), whereas for covalently bound ligands the top score was 45% (EnzyDock). These results suggest that one should perform in silico campaigns of Mpro with care and that more comprehensive strategies including ligand free energy perturbation might be necessary in conjunction with virtual screening and docking.

Cu(I) Controls Conformational States in Human Atox1 Metallochaperone: An EPR and Multiscale Simulation Study

Atox1 is a human copper metallochaperone that is responsible for transferring copper ions from the main human copper transporter, hCtr1, to ATP7A/B in the Golgi apparatus. Atox1 interacts with the Ctr1 C-terminal domain as a dimer, although it transfers the copper ions to ATP7A/B in a monomeric form. The copper binding site in the Atox1 dimer involves Cys12 and Cys15, while Lys60 was also suggested to play a role in the copper binding. We recently showed that Atox1 can adopt various conformational states, depending on the interacting protein. In the current study, we apply EPR experiments together with hybrid quantum mechanics–molecular mechanics molecular dynamics simulations using a recently developed semiempirical density functional theory approach, to better understand the effect of Atox1’s conformational states on copper coordination. We propose that the flexibility of Atox1 occurs owing to protonation of one or more of the cysteine residues, and that Cys15 is an important residue for Atox1 dimerization, while Cys12 is a critical residue for Cu(I) binding. We also show that Lys60 electrostatically stabilizes the Cu(I)–Atox1 dimer.

Adaptive control of laser-wakefield accelerators driven by mid-IR laser pulses

There has been growing interest both in studying high intensity ultrafast laser plasma interactions with adaptive control systems as well as using long wavelength driver beams. We demonstrate the coherent control of the dynamics of laser-wakefield acceleration driven by ultrashort (∼ 100 fs) mid-infrared (∼ 3.9 μm) laser pulses. The critical density at this wavelength is 7.3 × 10¹⁹ cm^-3, which is achievable with an ordinary gas target system. Interactions between mid-infrared laser pulses and such near-critical-density plasma may be beneficial due to much higher absorption of laser energy. In addition, the normalized vector potential of the laser field a₀ increases with longer laser wavelength, lowering the required peak laser intensity to drive non-linear laser-wakefield acceleration. Here, MeV level, collimated electron beams with non-thermal, peaked energy spectra are generated. Optimization of electron beam qualities are realized through adaptive control of the laser wavefront. A genetic algorithm controlling a deformable mirror improves the electron total charge, energy spectra, beam pointing and stability at various plasma density profiles. Particle-in-cell simulations reveal that the optimal wavefront causes an earlier injection on the density up-ramp and thus higher energy gain as well as less filamentation during the interaction, which leads to the improvement in electron beam collimation and energy spectra.

Laser wakefield acceleration with mid-IR laser pulses

We report on, to the best of our knowledge, the first results of laser plasma wakefield acceleration driven by ultrashort mid-infrared (IR) laser pulses (λ=3.9  μm, 100 fs, 0.25 TW), which enable near- and above-critical density interactions with moderate-density gas jets. Relativistic electron acceleration up to ∼12  MeV occurs when the jet width exceeds the threshold scale length for relativistic self-focusing. We present scaling trends in the accelerated beam profiles, charge, and spectra, which are supported by particle-in-cell simulations and time-resolved images of the interaction. For similarly scaled conditions, we observe significant increases in the accelerated charge, compared to previous experiments with near-infrared (λ=800  nm) pulses.

Novel morphological macular findings in juvenile CLN3 disease

AIMS

Juvenile CLN3 disease, one of the most common forms of a group of lysosomal storage diseases called neuronal ceroid lipofuscinoses (NCLs), is a progressive neurodegenerative disorder with initial visual deterioration. The objective of this study was to analyse the retinal phenotype of patients with CLN3 disease with the help of recent ophthalmic imaging modalities to distinguish CLN3 disease from other inherited retinal dystrophies.

METHODS

Patients underwent ophthalmic evaluations, including anterior and posterior segment examinations, optical coherence tomography, fundus autofluorescence, near infrared imaging and fundus photography. Patients were also assessed according to the Hamburg juvenile NCL (JNCL) score. Each ophthalmic finding was assessed by three independent examiners and assigned to a clinical severity score.

RESULTS

22 eyes of 11 patients were included. The mean age at examination was 14.4 years (range 11.8-26.4 years), with an average age at initial diagnosis of 8 years (range 4.5-11 years). The mean Hamburg JNCL score was 7.3 (range 0-13). All patients showed a specific macular striation pattern on optical coherence tomography that was independent of age and progression of the disease. Other previously described retinal features of CLN3 disease were classified into four severity grades.

CONCLUSIONS

This study represents the first prospective observational case series documenting retinal abnormalities in CLN3 disease with the aid of the spectral domain optical coherence tomography. The major finding was a characteristic, striated macular pattern in all patients studied. Particularly in early disease cases, macular striae can potentially help to discriminate CLN3 disease from other inherited forms of retinitis pigmentosa.

Multi-profile hidden Markov model for mood, dietary intake, and physical activity in an intervention study of childhood obesity

Motivated by an application to childhood obesity data in a clinical trial, this paper describes a multi-profile hidden Markov model (HMM) that uses several temporal chains of measures respectively related to psychosocial attributes, dietary intake, and energy expenditure behaviors of adolescents in a school setting. Using these psychological and behavioral profiles, the model delineates health states from the longitudinal data set. Furthermore, a two-level regression model that takes into account the clustering effects of students within school is used to assess the effects of school-based and community-based interventions and other risk factors on the transition between health states over time. The results from our study suggest that female students tend to decrease their physical activities despite a high level of anxiety about weight. The finding is consistent across intervention and control arms.

Study design and baseline description of the BMI2 trial: reducing paediatric obesity in primary care practices

OBJECTIVES

This study will test the efficacy of motivational interviewing (MI) conducted by primary care providers and dieticians among children ages 2-8 years old with a body mass index (BMI) ≥ 85th and ≤ 97th percentile.

METHODS

Forty-two practices from the American Academy of Pediatrics, Pediatric Research in Office Settings Network were assigned to one of three groups. Group 1 (usual care) measures BMI percentile at baseline, and at 1- and 2-year follow-ups and receives standard health education materials. Group 2 providers deliver three proactive MI counselling sessions with a parent of the index child in Year 1 and one additional 'booster' visit in Year 2. Group 3 adds six MI counselling sessions from a trained dietician. The primary outcome is the child's BMI percentile at 2-year follow-up. Secondary outcomes include parent report of the child's screen time, physical activity, intake of fruits and vegetables, and sugar-sweetened beverages.

RESULTS

We enrolled 633 eligible children whose mean BMI percentile was 92.0 and mean age of 5.1. The cohort was 57% female. Almost 70% of parents reported a household income of ≥ $40,000 per year, and 39% had at least a college education. The cohort was 63% white, 23% Hispanic, 7% black and 7% Asian. Parent self-reported confidence that their child will achieve a healthy weight was on average an 8 (out of 10).

CONCLUSION

To date, several aspects of the study can inform similar efforts including our ability to use volunteer clinicians to recruit participants and their willingness to dedicate their time, without pay, to receive training in MI.

Just enough, but not too much interactivity leads to better clinical skills performance after a computer assisted learning module

BACKGROUND

Well-designed computer-assisted instruction (CAI) can potentially transform medical education. Yet little is known about whether specific design features such as direct manipulation of the content yield meaningful gains in clinical learning. We designed three versions of a multimedia module on the abdominal exam incorporating different types of interactivity.

METHODS

As part of their physical diagnosis course, 162 second-year medical students were randomly assigned (1:1:1) to Watch, Click or Drag versions of the abdominal exam module. First, students' prior knowledge, spatial ability, and prior experience with abdominal exams were assessed. After using the module, students took a posttest; demonstrated the abdominal exam on a standardized patient; and wrote structured notes of their findings.

RESULTS

Data from 143 students were analyzed. Baseline measures showed no differences among groups regarding prior knowledge, experience, or spatial ability. Overall there was no difference in knowledge across groups. However, physical exam scores were significantly higher for students in the Click group.

CONCLUSIONS

A mid-range level of behavioral interactivity was associated with small to moderate improvements in performance of clinical skills. These improvements were likely mediated by enhanced engagement with the material, within the bounds of learners' cognitive capacity. These findings have implications for the design of CAI materials to teach procedural skills.

Regulated overexpression of the survival factor bcl-2 in CHO cells increases viable cell density in batch culture and decreases DNA release in extended fixed-bed cultivation

Using multicistronic expression technology we generated a stable Chinese hamster ovary (CHO) cell line (MG12) expressing a model secreted heterologous glycoprotein, the secreted form of the human placental alkaline phosphatase (SEAP), and bcl-2, best known as an apoptosis inhibitor, in a tetracycline-repressible dicistronic configuration. In batch cultivations in serum-containing medium, MG12 cells reached twice the final viable cell density when Bcl-2 was overexpressed (in the absence oftetracycline) compared to MG12 populations culturedunder tetracycline-containing conditions (bcl-2repressed). However, bcl-2-expressing MG12 cellsshowed no significant retardation of the decline phasecompared to batch cultures in which the dicistronicexpression unit was repressed.Genetic linkage of bcl-2 expression with the reporter protein SEAP in our multicistronic construct allowed online monitoring of Bcl-2 expression over an extended, multistage fixed-bed bioreactor cultivation. The cloned multicistronic expression unit proved to be stable over a 100 day bioreactor run. CHO MG12 cells in the fixed-bed reactor showed a drastic decrease in the release of DNA into the culture supernatant under conditions of reduced tetracycline (and hencederepressed SEAP and bcl-2 overexpression). This observation indicated enhanced robustness associated with bcl-2 overexpression, similar to recent findings for constitutive Bcl-2-overexpressing hybridoma cells under the same bioprocess conditions. These findings indicate, in these serum-containing CHO cell cultures, that overexpression of Bcl-2 results in desirable modifications in culture physiology.

EGFR, TS, and ERCC1 expression in penile squamous cancer (PSC)

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Background: PSC is an aggressive disease with devastating consequences. While near-universal EGFR overexpression has been documented, little is known about its clinical implications, and the potential role of KRAS mutations has not been described. In other tumor types, ERCC1 and TS expression are associated with response to platinum and 5FU chemotherapy, but have not yet been evaluated in PSC.

Methods: After IRB approval, 28 PSC patients treated at LAC-USC were identified with tumor specimens available. Testing for EGFR, TS, and ERCC1 expression relative to internal standard gene was performed by real-time RT-PCR and correlated with clinical features.

Results: The median age was 45 (30-78). There were 2 Black, 1 Asian, 1 White, and 15 Hispanic men; 9 had unspecified race. T stages included 4 Tis, 6 T1, 17 T2, and 9 T3; 11 men had lymph node (LN) involvement. No KRAS mutations were identified. EGFR had the highest relative expression (median 4.65, range 1.6-44.2), followed by TS (median 1.69, range 0.49-4.69); ERCC1 overexpression was rare (median 0.54, range 0.21-1.29). Higher EGFR expression was significantly associated with poor differentiation (median 12.5 compared to 3.6 for moderate/well differentiated tumors) on continuous (p=0.03 by Mann Whitney) and cut-point analysis using >7 (two- sided p=0.03 by Fisher's exact test) but did not correlate with stage. Stage > T2 showed a trend toward higher risk of LN involvement (p=0.06 by chi square). There was no correlation between differentiation and stage, and no significant correlation for ERCC1 or TS with grade or stage.

Conclusions: EGFR overexpression is common in PSC and correlates with tumor grade but not stage, suggesting it may be important for disease progression. The absence of KRAS mutations may portend responsiveness to EGFR- targeted therapy based on experience in other tumors. Low ERCC1 as an association with platinum response will be explored in an expanded cohort.

No significant financial relationships to disclose.

Final results of PX-171–003-A0, part 1 of an open-label, single-arm, phase II study of carfilzomib (CFZ) in patients (pts) with relapsed and refractory multiple myeloma (MM)

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Background: CFZ is a novel proteasome inhibitor of the epoxyketone class that exhibits a high level of proteasome selectivityand demonstrates antitumor activity in bortezomib (BTZ)-resistant MM pts in phase I studies. Methods: PX-171–003-A0 was an open-label, multicenter study that enrolled MM pts who relapsed from >2 prior therapies, failed BTZ and at least 1 immunomodulatory agent [thalidomide (THAL) or lenalidomide (LEN)], and were refractory to last treatment [progressing on or within 60 d of last therapy or <25% response to last therapy]. Pts received CFZ 20 mg/m2 IV d 1, 2, 8, 9, 15 and 16 every 28 d for up to 12 cycles (C). Clinical benefit response (CBR) was defined as MR or better. Results: 46 pts were enrolled, including 78% with progression on or within 60 d of last therapy and 22% with no response to last therapy. 39 pts completed at least 1 C of CFZ, had measurable M-protein, and were evaluable for response. Median prior therapies was 5 (range 2–15). 100% of pts received prior BTZ, 91% prior THAL, 89% prior LEN, and 83% prior stem cell transplant (SCT) and all had failed combinations including anthracyclines (80%) and/or alkylating agents (94%). Pts received a median of 3 C (range 1–12); 13 pts completed ≥6 C. CBR was 26% (10/39 eval pts), including 5 pts achieving PR and 5 pts achieving MR. 5 BTZ-refractory pts achieved MR or PR. Median TTP was 6.2 mo, the median DOR for the MR + PR was 7.4 mo. 8/10 pts achieved response during C1. 16 additional pts achieved SD for at least 6 wks. The most common adverse events were fatigue, anemia, thrombocytopenia, nausea, upper respiratory infection, increased creatinine and diarrhea. Peripheral neuropathy occured in < 10% of pts with 1 Gr 3 in a pt with pre-existing Gr 2. Conclusions: Single-agent CFZ achieved a TTP of > 6 mo in relapsed and refractory MM pts who failed available therapies. 26% of patients had at least an MR and median duration of >7 mo with this steroid- and anthracycline-sparing regimen. CFZ toxicities were manageable and importantly, exacerbation of pre-existing PN was rare. The study has been expanded to enroll an additional 250 pts in this unmet medical need population at an escalated dose, and treatment has been extended beyond a year.

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