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Computational protein design is advancing rapidly. Here we describe efficient routes starting from validated parallel and antiparallel peptide assemblies to design two families of α-helical barrel proteins with central channels that bind small molecules. Computational designs are seeded by the sequences and structures of defined de novo oligomeric barrel-forming peptides, and adjacent helices are connected by loop building. For targets with antiparallel helices, short loops are sufficient. However, targets with parallel helices require longer connectors; namely, an outer layer of helix–turn–helix–turn–helix motifs that are packed onto the barrels. Throughout these computational pipelines, residues that define open states of the barrels are maintained. This minimizes sequence sampling, accelerating the design process. For each of six targets, just two to six synthetic genes are made for expression in Escherichia coli. On average, 70% of these genes express to give soluble monomeric proteins that are fully characterized, including high-resolution structures for most targets that match the design models with high accuracy.

We implement and interpret various supervised learning experiments involving real quadratic fields with class numbers 1, 2 and 3. We quantify the relative difficulties in separating class numbers of matching/different parity from a data-scientific perspective, apply the methodology of feature analysis and principal component analysis, and use symbolic classification to develop machine-learned formulas for class numbers 1, 2 and 3 that apply to our dataset.

Dual-emission fluorescence probes that provide high sensitivity are key for biomedical diagnostic applications. Nontoxic carbon dots (CDs) are an emerging alternative to traditional fluorescent probes; however, robust and reproducible synthetic strategies are still needed to access materials with controlled emission profiles and improved fluorescence quantum yields (FQYs). Herein, we report a practical and general synthetic strategy to access dual-emission CDs with FQYs as high as 0.67 and green/blue, yellow/blue, or red/blue excitation-dependent emission profiles using common starting materials such as citric acid, cysteine, and co-dopants to bias the synthetic pathway. Structural and physicochemical analysis using nuclear magnetic resonance, absorbance and fluorescence spectroscopy, Fourier-transform infrared spectroscopy, and X-ray photoelectron spectroscopy in addition to transmission electron and atomic force microscopy (TEM and AFM) is used to elucidate the material’s composition which is responsible for the unique observed photoluminescence properties. Moreover, the utility of the probes is demonstrated in the clinical setting by the synthesis of green/blue emitting antibody-CD conjugates which are used for the immunohistochemical staining of human brain tissues of glioblastoma patients, showing detection under two different emission channels.

Despite many decades of study, the excited state photophysics of polyenes remains controversial. In diphenylpolyenes with conjugated backbones that contain between 2 and 4 double carbon–carbon bonds, the first two excited electronic states are nearly degenerate but of entirely different character, and their energy splitting is strongly dependent on solvent polarizability. To examine the interplay between these different states, steady-state and time-resolved fluorescence spectroscopies were used to undertake a comprehensive investigation of diphenylocatetraene’s (DPO) excited state dynamics in 10 solvents of different polarizabilities and polarities, ranging from weakly interacting alkanes to polar hydrogen-bonding alcohols. These data revealed that photopreparation of the optically bright 1Bustate resulted in fast (<170 ps) internal conversion to the lower-lying optically dark 2Agstate. The 2Agstate is responsible for almost all the observed DPO fluorescence and gains oscillator strength via vibronic intensity stealing with the near-degenerate 1Bustate. The fluorescence lifetime associated with the 2Agstate decayed monoexponentially (4.2–7.2 ns) in contrast to prior biexponential decay kinetics reported for similar polyenes, diphenylbutadiene and diphenylhexatriene. An analysis combining the measured fluorescence lifetimes and fluorescence quantum yields (the latter varying between 7 and 21%) allowed for a 190 cm–1Herzberg–Teller vibronic coupling constant between the 1Buand 2Agstates to be determined. The analysis also revealed that the ordering of electronic states remains constant in all the solvents studied, with the 2Agstate minimum always lower in energy than that of the 1Bustate, thus making it a relatively simple polyene compared to structurally similar diphenylhexatriene.

The 2014–2017 global coral bleaching event caused widespread coral mortality; however, its impact on the capacity for coral reefs to maintain calcium carbonate structures has not been determined. Here, we quantified remotely sensed maximum heat stress during the 2014–2017 bleaching event, census‐based net carbonate budgets from benthic imagery and fish survey data, and net reef calcification from salinity normalized seawater total alkalinity anomalies collected from 2017–2019 for 56 Pacific coral reef sites (Mariana Islands, Northwestern Hawaiian Islands, Pacific Remote Island Areas, and American Samoa). We incorporated the census‐based and chemistry‐based metrics to determine a calcification vulnerability index for each site to maintain calcium carbonate balance to provide accessible information to managers and policy makers. Most coral reef sites likely experienced ecologically severe (79%, n= 44) or significant (9%, n= 7) heat stress during the 2014–2017 coral bleaching event. Census‐based net carbonate budgets (mean ± 95% = 2.1 ± 0.6 kg CaCO3m−2yr−1) were positive for 77% of sites (n= 43), neutral for 16% of sites (n= 9), and negative for 7% of sites (n= 4). Chemistry‐based relative net reef calcification (mean ± 95% = 22 ± 10 μmol kg−1) was positive for 84% of sites (n= 47), neutral for 11% of sites (n= 6), and negative for 5% of sites (n= 3). The calcification vulnerability index suggested the Pacific Ocean reef sites surveyed were of minimal (68%, n= 38) to moderate (32%, n= 18) concern for maintaining calcium carbonate balance following the bleaching event. This suggests that many reefs maintained positive calcium carbonate balance, but that a large number of reefs may be approaching a potential threshold for maintaining their calcium carbonate balance under the climate crisis.

Pharmacogenomics is a pillar of personalized medicine that has the potential to deliver optimized treatment in many medical settings. Military medicine in the deployed setting is unique and therefore warrants separate assessment pertaining to its potential capabilities and impact. Pharmacogenomics for United States Active Duty Service Members medical care in the deployed setting has not, to our knowledge, been previously reviewed. We present potential applications of pharmacogenomics to forward medical care through two comprehensive references for deployed medical care, the Tactical Combat Casualty Care Guidelines (TCCC) and Emergency War Surgery (EWS) fifth edition. All drugs within the deployment manuals, TCCC guidelines and EWS book, were identified and the list was cross-referenced to the Clinical Pharmacogenetics Implementation Consortium guidelines and genes–drugs interactions list as well as the Food and Drug Administration Table of Pharmacogenomics Biomarkers in Drug Labeling. Ten pharmacologic categories were identified, consisting of 15 drugs, along with the classes, aminogylcosides, beta-blockers, and volatile anesthetics. Drugs and pharmacogenomics liabilities were tabulated. Eight specific drugs or classes are expounded upon given the belief of the authors of their potential for impacting future treatment on the battlefield in the setting of prolonged field care. This review outlines several genes with liabilities in the prolonged field care setting and areas that may produce improved care with further study.

Pharmacogenomics (PGx) plays a fundamental role in personalized medicine, providing an evidence-based treatment approach centered on the relationship between genomic variations and their effect on drug metabolism. Cytochrome P450 (CYP450) enzymes are responsible for the metabolism of most clinically prescribed drugs and a major source of variability in drug pharmacokinetics and pharmacodynamics. To assess the prevalence of PGx testing within the Military Health System (MHS), testing of specific CYP450 enzymes was evaluated. Data were retrospectively obtained from the Military Health System Management Analysis and Reporting Tool (M2) database. Patient demographics were identified for each test, along with TRICARE status, military treatment facility, clinic, and National Provider Identifier. A total of 929 patients received 1,833 PGx tests, predominantly composed of active duty/guard service members (N= 460; 49.5%), with highest testing rates in the army (51.5%). An even distribution in testing was observed among gender, with the highest rates in Caucasians (41.7%). Of the CYP enzymes assessed, CYP2C19 and CYP2D6 accounted for 87.8% of all PGx CYP testing. The majority of patients were tested in psychiatry clinics (N= 496; 53.4%) and primary care clinics (N= 233; 25.1%), accounting for 56.4% and 24.8% of all tests, respectively. Testing was found to be provider driven, suggesting a lack of a standardized approach to PGx and its application in patient care within the MHS. We initially recommend targeted education and revising testing labels to be more uniform and informative. Long-term recommendations include establishing pharmacy-driven protocols and point-of-care PGx testing to optimize patient outcomes.

Starting from the zygote, all cells in the human body continuously acquire mutations. Mutations shared between different cells imply a common progenitor and are thus naturally occurring markers for lineage tracing1,2. Here we reconstruct extensive phylogenies of normal tissues from three adult individuals using whole-genome sequencing of 511 laser capture microdissections. Reconstructed embryonic progenitors in the same generation of a phylogeny often contribute to different extents to the adult body. The degree of this asymmetry varies between individuals, with ratios between the two reconstructed daughter cells of the zygote ranging from 60:40 to 93:7. Asymmetries pervade subsequent generations and can differ between tissues in the same individual. The phylogenies resolve the spatial embryonic patterning of tissues, revealing contiguous patches of, on average, 301 crypts in the adult colonic epithelium derived from a most recent embryonic cell and also a spatial effect in brain development. Using data from ten additional men, we investigated the developmental split between soma and germline, with results suggesting an extraembryonic contribution to primordial germ cells. This research demonstrates that, despite reaching the same ultimate tissue patterns, early bottlenecks and lineage commitments lead to substantial variation in embryonic patterns both within and between individuals.

Over the course of an individual’s lifetime, normal human cells accumulate mutations1. Here we compare the mutational landscape in 29 cell types from the soma and germline using multiple samples from the same individuals. Two ubiquitous mutational signatures, SBS1 and SBS5/40, accounted for the majority of acquired mutations in most cell types, but their absolute and relative contributions varied substantially. SBS18, which potentially reflects oxidative damage2, and several additional signatures attributed to exogenous and endogenous exposures contributed mutations to subsets of cell types. The rate of mutation was lowest in spermatogonia, the stem cells from which sperm are generated and from which most genetic variation in the human population is thought to originate. This was due to low rates of ubiquitous mutational processes and may be partially attributable to a low rate of cell division in basal spermatogonia. These results highlight similarities and differences in the maintenance of the germline and soma.

The cellular landscape of the human intestinal tract is dynamic throughout life, developing in utero and changing in response to functional requirements and environmental exposures. Here, to comprehensively map cell lineages, we use single-cell RNA sequencing and antigen receptor analysis of almost half a million cells from up to 5 anatomical regions in the developing and up to 11 distinct anatomical regions in the healthy paediatric and adult human gut. This reveals the existence of transcriptionally distinct BEST4 epithelial cells throughout the human intestinal tract. Furthermore, we implicate IgG sensing as a function of intestinal tuft cells. We describe neural cell populations in the developing enteric nervous system, and predict cell-type-specific expression of genes associated with Hirschsprung’s disease. Finally, using a systems approach, we identify key cell players that drive the formation of secondary lymphoid tissue in early human development. We show that these programs are adopted in inflammatory bowel disease to recruit and retain immune cells at the site of inflammation. This catalogue of intestinal cells will provide new insights into cellular programs in development, homeostasis and disease.

Global concern over widely documented declines in pollinators1–3has led to the identification of anthropogenic stressors that, individually, are detrimental to bee populations4–7. Synergistic interactions between these stressors could substantially amplify the environmental effect of these stressors and could therefore have important implications for policy decisions that aim to improve the health of pollinators3,8,9. Here, to quantitatively assess the scale of this threat, we conducted a meta-analysis of 356 interaction effect sizes from 90 studies in which bees were exposed to combinations of agrochemicals, nutritional stressors and/or parasites. We found an overall synergistic effect between multiple stressors on bee mortality. Subgroup analysis of bee mortality revealed strong evidence for synergy when bees were exposed to multiple agrochemicals at field-realistic levels, but interactions were not greater than additive expectations when bees were exposed to parasites and/or nutritional stressors. All interactive effects on proxies of fitness, behaviour, parasite load and immune responses were either additive or antagonistic; therefore, the potential mechanisms that drive the observed synergistic interactions for bee mortality remain unclear. Environmental risk assessment schemes that assume additive effects of the risk of agrochemical exposure may underestimate the interactive effect of anthropogenic stressors on bee mortality and will fail to protect the pollinators that provide a key ecosystem service that underpins sustainable agriculture.

Tracing produced water origins from wells hydraulically fractured with freshwater-based fluids is sometimes predicated on assumptions that (1) each geological formation contains compositionally unique brine and (2) produced water from recently hydraulically fractured wells resembles fresher meteoric water more so than produced water from older wells. These assumptions are not valid in Williston Basin oil wells sampled in this study. Although distinct average 228Ra/226Ra ratios were found in water produced from the Bakken and Three Forks Formations, average δ2H, δ18O, specific gravity, and conductivity were similar but exhibited significant variability across five oil fields within each formation. Furthermore, initial produced water (“flowback”) was operationally defined based on the presence of glycol ether compounds and water from wells that had produced <56% of the amount of fluids injected and sampled within 160 days of fracturing. Flowback unexpectedly exhibited higher temperature, specific gravity, conductivity, δ2H, and δ18O, but lower oxidation–reduction potential and δ11B, relative to the wells thought to be producing formation brines (from wells with a produced-to-injected water ratio [PIWR] > 0.84 and sampled more than 316 days after fracturing). As such, establishing an overall geochemical and isotopic signature of produced water compositions based solely on chemical similarity to meteoric water and formation without the consideration of well treatments, well completion depth, or lateral location across the basin could be misleading if these signatures are assumed to be applicable across the entire basin. These findings have implications for using produced water compositions to understand the interbasin fluid flow and trace sources of hydraulic fracturing fluids.

ABSTRACTIntroductionThe fibroblast growth factor receptor (FGFR) pathway is essential in cell proliferation, differentiation, migration, and survival. Cancers such as intrahepatic cholangiocarcinoma (IHCA) have demonstrated alterations of FGFR allowing unregulated growth. Infigratinib (BGJ398) is a potent ATP-competitive inhibitor of all four FGFR receptors as demonstrated by the consistently high prevalence of hyperphosphatemia, indicating disruption of FGFR-related phosphate homeostasis.Areas coveredIn this article, the authors discuss preclinical studies and the biological characterization of BGJ398 that inspired its investigation for cancer treatment. They summarize results from phase I and II studies and comment on ongoing phase III clinical trials primarily focusing on its role in treating IHCA.Expert opinionInfigratinib exhibits high potency FGFR1-3 inhibition in preclinical studies. Clinically, agents targeting FGFR including infigratinib show promising anti-tumor activity in targeted trials. Pemigatinib, an FGFR inhibitor, has recently been approved by the FDA for use in refractory IHCA. We believe infigratinib represents a promising agent in the treatment of refractory IHCA with FGFR2 fusions and is uniquely positioned to be a potential option in chemonaive patient populations. An ongoing phase III trial (PROOF-301) compares the efficacy and safety of infigratinib versus standard gemcitabine and cisplatin in untreated patients with IHCA and FGFR2 fusions.

The photochemical dynamics of three classes of organic photoredox catalysts employed in organocatalyzed atom-transfer radical polymerization (O-ATRP) are studied using time-resolved optical transient absorption and fluorescence spectroscopy. The nine catalysts selected for study are examples of N-aryl and core-substituted dihydrophenazine, phenoxazine and phenothiazine compounds with varying propensities for control of polymerization outcomes. Excited singlet-state lifetimes extracted from the spectroscopic measurements are reported in N,N-dimethylformamide (DMF), dichloromethane (DCM), and toluene. Ultrafast (<200 fs to 3 ps) electronic relaxation of the photocatalysts after photoexcitation at near-UV wavelengths (318–390 nm) populates the first singlet excited state (S1). The S1-state lifetimes range from 130 ps to 40 ns with a considerable dependence on the photocatalyst structure and the solvent. The competition between ground electronic state recovery and intersystem crossing controls triplet state populations and is a minor pathway in the dihydrophenazine derivatives but is of greater importance for phenoxazine and phenothiazine catalysts. A comparison of our results with previously reported O-ATRP performances of the various photoredox catalysts shows that high triplet-state quantum yields are not a prerequisite for controlling polymer dispersity. For example, the photocatalyst 5,10-bis(4-cyanophenyl)-5,10-dihydrophenazine, shown previously to exert good polymerization control, possesses the shortest S1-state lifetime (135 ps in DMF and 180 ps in N,N-dimethylacetamide) among the nine examples reported here and a negligible triplet-state quantum yield. The results call for a re-evaluation of the excited-state properties of most significance in governing the photocatalytic behavior of organic photoredox catalysts in O-ATRP reactions.

Placentas can exhibit chromosomal aberrations that are absent from the fetus1. The basis of this genetic segregation, which is known as confined placental mosaicism, remains unknown. Here we investigated the phylogeny of human placental cells as reconstructed from somatic mutations, using whole-genome sequencing of 86 bulk placental samples (with a median weight of 28 mg) and of 106 microdissections of placental tissue. We found that every bulk placental sample represents a clonal expansion that is genetically distinct, and exhibits a genomic landscape akin to that of childhood cancer in terms of mutation burden and mutational imprints. To our knowledge, unlike any other healthy human tissue studied so far, the placental genomes often contained changes in copy number. We reconstructed phylogenetic relationships between tissues from the same pregnancy, which revealed that developmental bottlenecks genetically isolate placental tissues by separating trophectodermal lineages from lineages derived from the inner cell mass. Notably, there were some cases with full segregation—within a few cell divisions of the zygote—of placental lineages and lineages derived from the inner cell mass. Such early embryonic bottlenecks may enable the normalization of zygotic aneuploidy. We observed direct evidence for this in a case of mosaic trisomic rescue. Our findings reveal extensive mutagenesis in placental tissues and suggest that mosaicism is a typical feature of placental development.

Personalized medicine is the right treatment, to the right patient, at the right dose. Knowledge of genetic predisposition to variable metabolism and distribution of drugs within the body is currently available as pharmacogenomic testing and is one of the pillars of personalized medicine. Pharmacogenomic testing is growing. It has become part of guidelines for dosing on FDA labels and has been used by health care organizations to improve outcomes and reduce adverse events. Additionally, it has been FDA approved for direct-to-consumer purchase and has been cause of concern of patient self-dosing and medication changes. Presumably in the near future, pharmacogenomics will be impressed upon the military health system (MHS) provider from either a top-down, command requested, or from a bottom-up, patient requested, approach. To date, widespread implementation of pharmacogenomic testing does not seem to be established within the MHS. This survey sheds light on the knowledge, exposure, use, comfort, and interest among family medicine providers in the MHS. It compares similar results in other national and international surveys and compares results among a small subset of residents to staff.

Coral reef calcification is expected to decline due to climate change stressors such as ocean acidification and warming. Projections of future coral reef health are based on our understanding of the environmental drivers that affect calcification and dissolution. One such driver that may impact coral reef health is heterotrophy of oceanic‐sourced particulate organic matter, but its link to calcification has not been directly investigated in the field. In this study, we estimated net ecosystem calcification and oceanic particulate organic carbon (POCoc) uptake across the Kāne'ohe Bay barrier reef in Hawai'i. We show that higher rates of POCocuptake correspond to greater net ecosystem calcification rates, even under low aragonite saturation states (Ωar). Hence, reductions in offshore productivity may negatively impact coral reefs by decreasing the food supply required to sustain calcification. Alternatively, coral reefs that receive ample inputs of POCocmay maintain higher calcification rates, despite a global decline in Ωar. Coral reefs are threatened by climate change stressors including ocean acidification and ocean warming. One way to measure and monitor coral reef health is to estimate coral reef calcification, which is influenced by several environmental factors including light, temperature, pH, and nutrient availability. By understanding the effects of these factors on calcification, we can better predict how corals will respond to climate change. One potentially important factor for calcification that has not been investigated in the field is coral reef ecosystem feeding on particulate organic matter supplied from offshore (i.e., oceanic particulate organic matter). In this study, we estimated net ecosystem calcification and oceanic particulate organic carbon (POC) uptake across the Kāne'ohe Bay barrier reef in Hawai'i. For the first time, we show a direct correlation between net ecosystem calcification and oceanic POC uptake, which suggests that the reef is using oceanic POC as an energy source to elevate calcification. However, since climate change reduces oceanic POC production through warming and stratification, our results imply coral reef calcification may decline. Alternatively, coral reefs located in regions of high oceanic productivity and that sustain greater rates of oceanic POC uptake may be able to maintain calcification longer into the future. Oceanic particulate organic matter uptake elevates net ecosystem calcification, even under low aragonite saturation statesThe rates of net ecosystem calcification and oceanic particulate organic matter uptake are sensitive to changes in water flow speeds

The ultrafast dynamics of a bimolecular excited-state proton transfer (ESPT) reaction between the photoacid 7-hydroxy-4-(trifluoromethyl)-1-coumarin (CouOH) and 1-methylimidazole (MI) base in aprotic chloroform-d1solution were investigated using ultrafast transient infrared (TRIR) and transient absorption (TA) spectroscopies. The excited-state lifetime of the photoacid in solution is relatively short (52 ps), which at the millimolar photoacid and base concentrations used in our study precludes any diffusion-controlled bimolecular ESPT reactions. This allows the prompt ESPT reaction between hydrogen-bonded CouOH and MI molecules to be studied in isolation and the “contact” ESPT dynamics to be unambiguously determined. Our time-resolved studies reveal that ultrafast ESPT from the CouOH moiety to hydrogen-bonded MI molecules occurs within ∼1 ps, tracked by unequivocal spectroscopic signatures of CouO–* photoproducts that are formed in tandem with HMI+. Some of the ESPT photoproducts subsequently π-stack to form exciplexes on a ∼35 ps time scale, minimizing the attractive Coulombic forces between the oppositely charged aromatic molecules. For the concentrations of CouOH and MI used in our study (up to 8 mM), we saw no evidence for excited-state tautomerization of coumarin anions.

A 32-year-old male developed neuropsychiatric symptoms 2 weeks after starting mefloquine 250 mg/week for malaria prophylaxis. He continued to take the medication for the next 4 months. Initial symptoms included vivid dreams and anxiety, as well as balance problems. These symptoms persisted and progressed over the next 4 years to include vertigo, emotional lability, and poor short-term memory, which have greatly affected his personal and professional life. An extensive evaluation revealed objective evidence supporting a central vestibulopathy. These symptoms have been unresponsive to pharmacologic therapy and psychotherapy. A Naranjo assessment score of 6 was obtained for his initial symptoms, indicating a probable adverse drug reaction to mefloquine given the relationship between the clinical picture and drug exposure.

Background. Translational research seeks to build bridges between research and practice to address public health issues efficiently and effectively. The purpose of this article was to evaluate a newly formed institute that provided graduate students and adolescent behavioral health community professionals with a translational research service-learning opportunity through the creation of a community–university mentoring partnership. Goals of the team-based research mentorship approach included (1) providing students the skills for implementing translational research, (2) providing research opportunities for community agencies to enhance operations and to encourage ongoing research involvement, and (3) developing relationships between university faculty and community agency professionals for further research collaborations. Method. The Institute used the National Institute on Drug Abuse’s Mentoring Mosaic to select a diverse group of community and academic mentors. The research mentorship experience of the initial cohort was evaluated based on the Research Mentorship Conceptual Framework and Self-Assessment Tool. Results. As a direct result of the research mentorship, outcomes for the academic and community mentors and scholars (i.e., those seeking a graduate certificate) included improved working relationships/networking and research experience. Through experiential learning, scholars also discovered career trajectory clarity, the need for community collaboration in research, opportunities for continuing professional development, a greater understanding of public health competencies and how they align with community-based research, and skill development in best practices for translational research. Conclusion. The team mentoring approach is a form of pedagogy that holds promise to enhance translational research and community-based research efforts while developing public health competencies.