Design of proteasome inhibitors with oral efficacy in vivo against Plasmodium falciparum and selectivity over the human proteasome.

The Plasmodium falciparum proteasome is a potential antimalarial drug target. We have identified a series of amino-amide boronates that are potent and specific inhibitors of the P. falciparum 20S proteasome (Pf20S) ß5 active site and that exhibit fast-acting antimalarial activity. They selectively inhibit the growth of P. falciparum compared with a human cell line and exhibit high potency against field isolates of P. falciparum and Plasmodium vivax They have a low propensity for development of resistance and possess liver stage and transmission-blocking activity. Exemplar compounds, MPI-5 and MPI-13, show potent activity against P. falciparum infections in a SCID mouse model with an oral dosing regimen that is well tolerated. We show that MPI-5 binds more strongly to Pf20S than to human constitutive 20S (Hs20Sc). Comparison of the cryo-electron microscopy (EM) structures of Pf20S and Hs20Sc in complex with MPI-5 and Pf20S in complex with the clinically used anti-cancer agent, bortezomib, reveal differences in binding modes that help to explain the selectivity. Together, this work provides insights into the 20S proteasome in P. falciparum, underpinning the design of potent and selective antimalarial proteasome inhibitors.

The First Hybrid International Educational Comprehensive Cleft Care Workshop.

OBJECTIVE: Describe the first hybrid global simulation-based comprehensive cleft care workshop, evaluate impact on participants, and compare experiences based on in-person versus virtual attendance. DESIGN: Cross-sectional survey-based evaluation. SETTING: International comprehensive cleft care workshop. PARTICIPANTS: Total of 489 participants. INTERVENTIONS: Three-day simulation-based hybrid comprehensive cleft care workshop. MAIN OUTCOME MEASURES: Participant demographic data, perceived barriers and interventions needed for global comprehensive cleft care delivery, participant workshop satisfaction, and perceived short-term impact on practice stratified by in-person versus virtual attendance. RESULTS: The workshop included 489 participants from 5 continents. The response rate was 39.9%. Participants perceived financial factors (30.3%) the most significant barrier and improvement in training (39.8%) as the most important intervention to overcome barriers facing cleft care delivery in low to middle-income countries. All participants reported a high level of satisfaction with the workshop and a strong positive perceived short-term impact on their practice. Importantly, while this was true for both in-person and virtual attendees, in-person attendees reported a significantly higher satisfaction with the workshop (28.63 ± 3.08 vs 27.63 ± 3.93; P = .04) and perceived impact on their clinical practice (22.37 ± 3.42 vs 21.02 ± 3.45 P = .01). CONCLUSION: Hybrid simulation-based educational comprehensive cleft care workshops are overall well received by participants and have a positive perceived impact on their clinical practices. In-person attendance is associated with significantly higher satisfaction and perceived impact on practice. Considering that financial and health constraints may limit live meeting attendance, future efforts will focus on making in-person and virtual attendance more comparable.

A Clinical Report Utilizing the VITOM 3D® Microvideoscope for Cleft Palate Repair.

Cleft palate surgery has traditionally presented numerous problems for cleft surgeons including ergonomics, limited visual fields restricting the opportunity for demonstration and teaching. Additionally, the move toward online teaching means the ability to record or livestream video is paramount. The following report of eight cleft palate repairs highlights the novel use of the Vitom 3D® microvideoscope as an innovative technique for cleft palate repair with our early experience demonstrating significant ergonomic and teaching benefits.

Species-Specific Characteristics Influence Contaminant Accumulation Trajectories and Signatures Across Ontogeny in Three Pelagic Shark Species.

Factors influencing organic contaminant accumulation in sharks, especially across ontogeny, are not well-known. Contaminant concentrations were measured in three species of sharks (Blue, Shortfin Mako, and Common Thresher) across a range of size classes (neonatal to adult) that vary in their ecological and physiological characteristics. Empirical data was compared to a theoretical framework that predicted the shape of lifetime accumulation curves. We found that a one-size-fits-all accumulation model was not appropriate as species-specific characteristics had a significant effect on contaminant accumulation trajectories. Maternal offloading likely has an important effect on determining neonatal shark contaminant starting points, and trophic ecology and physiology may interact to affect the shape of species' contaminant accumulation curves. Makos were found to have the highest accumulation potential and Blues the lowest, with Threshers being intermediate in accumulation potential. Changes in species' ecology and/or physiology were also reflected in contaminant signature changes over ontogeny. If contaminant concentrations are to be used as a proxy for risk, species-specific characteristics need to be taken into account when estimating contaminant exposure and its potential negative effects on shark health and human consumption safety.

A Low-Cost Continuous Turbidity Monitor.

Turbidity describes the cloudiness, or clarity, of a liquid. It is a principal indicator of water quality, sensitive to any suspended solids present. Prior work has identified the lack of low-cost turbidity monitoring as a significant hurdle to overcome to improve water quality in many domains, especially in the developing world. Low-cost hand-held benchtop meters have been proposed. This work adapts and verifies the technology for continuous monitoring. Lab tests show the low-cost continuous monitor can achieve 1 nephelometric turbidity unit (NTU) accuracy in the range 0-100 NTU and costs approximately 64 USD in components to construct. This level of accuracy yields useful and actionable data about water quality and may be sufficient in certain applications where cost is a primary constraint. A 38-day continuous monitoring trial, including a step change in turbidity, showed promising results with a median error of 0.45 and 1.40 NTU for two different monitors. However, some noise was present in the readings resulting in a standard deviation of 1.90 and 6.55 NTU, respectively. The cause was primarily attributed to ambient light and bubbles in the piping. By controlling these noise sources, we believe the low-cost continuous turbidity monitor could be a useful tool in multiple domains.

Adaptation and application of multivariate AMBI (M-AMBI) in US coastal waters.

The multivariate AMBI (M-AMBI) is an extension of the AZTI Marine Biotic Index (AMBI) that has been used extensively in Europe, but not in the United States. In a previous study, we adapted AMBI for use in US coastal waters (US AMBI), but saw biases in salinity and score distribution when compared to locally calibrated indices. In this study we modified M-AMBI for US waters and compared its performance to that of US AMBI. Index performance was evaluated in three ways: 1) concordance with local indices presently being used as management tools in three geographic regions of US coastal waters, 2) classification accuracy for sites defined a priori as good or bad and 3) insensitivity to natural environmental gradients. US M-AMBI was highly correlated with all three local indices and removed the compression in response seen in moderately disturbed sites with US AMBI. US M-AMBI and US AMBI did a similar job correctly classifying sites as good or bad in local validation datasets (83 to 100% accuracy vs. 84 to 95%, respectively). US M-AMBI also removed the salinity bias of US AMBI so that lower salinity sites were not more likely to be incorrectly classified as impaired. The US M-AMBI appears to be an acceptable index for comparing condition across broad-scales such as estuarine and coastal waters surveyed by the US EPA's National Coastal Condition Assessment, and may be applicable to areas of the US coast that do not have a locally derived benthic index.

Programmed death ligand 1 expression in triple-negative breast cancer is associated with tumour-infiltrating lymphocytes and improved outcome.

AIMS: Triple-negative breast cancer (TNBC) patients generally have a poor outcome; there is a pressing need to identify more effective therapeutic strategies. Clinical trials targeting programmed death 1/programmed death ligand 1 (PD1/PDL1) in melanoma and non-small-cell lung cancer have reported high response rates, and tumoral PDL1 expression has been suggested as a potential biomarker to enrich for patient response to these treatments. There are only very limited data to date reporting the expression of PDL1 in TNBC. METHODS AND RESULTS: PDL1 immunohistochemistry was performed on 161 primary TNBCs and assessed in the tumour as well as immune cells in the stromal compartment. PDL1 expression was very common in TNBC, expressed in the tumour cell membrane (64%), cytoplasm (80%) and stromal (93%) cellular compartments. Cytoplasmic tumoral expression of PDL1 was associated with a lower risk of breast cancer-specific death [hazard ratio (HR) 0.45, P = 0.035] while stromal PDL1 expression was associated with a lower rate of deaths from all causes (HR 0.305, P = 0.0042). Membranous expression of PDL1 was not associated with outcome. While both PDL1 expression and tumour-infiltrating lymphocytes were associated with a better outcome, only lymphovascular invasion and high tumour-infiltrating lymphocytes were independently prognostic for breast cancer-specific death. CONCLUSION: While PDL1 expression is frequent in TNBC, it was not independently prognostic. There were differences in outcome depending on the cellular compartment of PDL1 expression. These data provide further impetus for investigating the utility of immune checkpoint therapies in TNBC, given the clinical significance of tumour-infiltrating lymphocytes (TILs) and PDL1 expression in this cohort.

Hospitalisations up to adulthood for children born with orofacial clefts.

AIM: The aim of this study was to compare hospital admissions from infancy to adulthood, between children born with orofacial clefts (OFC) and those without OFC. METHODS: The method used was a cohort study using record-linked administrative datasets. Participants included all children liveborn in Western Australia (WA) between 1980 and 2010 diagnosed with OFC, who were frequency matched by year of birth to randomly selected liveborn children without OFC. We calculated rate ratios (RR) of hospital admission, number and reason of admissions, cumulative length of stay, for each cleft type (cleft lip only (CLO), cleft lip and palate (CL+P), cleft palate only (CPO), no OFC) and by age period (infancy, pre-school, primary and high school ages, and early adulthood). RESULTS: Overall, 1396 children were diagnosed with an OFC and compared with 6566 children without OFC. Individuals born with OFC were up to three times more likely to be admitted to hospital, had more admissions and longer cumulative length of stay in all age periods. Children with OFC were also more likely to be admitted for ear and digestive system conditions (RR up to 30 and six times higher, respectively). Children with CL+P and CPO were more likely to be admitted for respiratory conditions (RR 1.3-2.0) and children with CPO were six times more likely to be admitted for care for other congenital anomalies. CONCLUSIONS: Throughout childhood, individuals born with OFC were more likely to be admitted, and had more hospitalisations than those without OFC. Children born with CL+P or CPO had a higher hospitalisation burden than children born with CLO.

Phenotyping: targeting genotype's rich cousin for diagnosis.

There are many current and evolving tools to assist clinicians in their daily work of phenotyping. In medicine, the term 'phenotype' is usually taken to mean some deviation from normal morphology, physiology and behaviour. It is ascertained via history, examination and investigations, and a primary aim is diagnosis. Therefore, doctors are, by necessity, expert 'phenotypers'. There is an inherent and partially realised power in phenotypic information that when harnessed can improve patient care. Furthermore, phenotyping developments are increasingly important in an era of rapid advances in genomic technology. Fortunately, there is an expanding network of phenotyping tools that are poised for clinical translation. These tools will preferentially be implemented to mirror clinical workflows and to integrate with advances in genomic and information-sharing technologies. This will synergise with and augment the clinical acumen of medical practitioners. We outline key enablers of the ascertainment, integration and interrogation of clinical phenotype by using genetic diseases, particularly rare ones, as a theme. Successes from the test bed or rare diseases will support approaches to common disease.

The facial evolution: looking backward and moving forward.

Three-dimensional (3D) facial analysis is ideal for high-resolution, nonionizing, noninvasive objective, high-throughput phenotypic, and phenomic studies. It is a natural complement to (epi)genetic technologies to facilitate advances in the understanding of rare and common diseases. The face is uniquely reflective of the primordial tissues, and there is evidence supporting the application of 3D facial analysis to the investigation of variation and disease including studies showing that the face can reflect systemic health, provides diagnostic clues to disorders, and that facial variation reflects biological pathways. In addition, facial variation has been related to evolutionary factors. The purpose of this review is to look backward to suggest that knowledge of human evolution supports, and may instruct, the application and interpretation of studies of facial morphology for documentation of human variation and investigation of its relationships with health and disease. Furthermore, in the context of advances of deep phenotyping and data integration, to look forward to suggest approaches to scalable implementation of facial analysis, and to suggest avenues for future research and clinical application of this technology.

Dental arch relationship outcomes in children with complete unilateral cleft lip and palate treated at Princess Margaret Hospital for Children, Perth, Western Australia.

OBJECTIVES: To (1) audit dental arch relationships of all children born between 1982 and 1999 with complete unilateral cleft lip and palate (UCLP) treated at the Cleft Lip and Palate Unit, Princess Margaret Hospital for Children (PMH), Perth, Western Australia, (2) assess the distribution of GOSLON ratings from dental casts taken at 9 years, (3) compare the 9-year GOSLON ratings for "High" and "Low" caseload surgeons, and (4) compare the 9-year PMH GOSLON ratings with published ratings from other units. DESIGN: Retrospective audit of dental casts and medical charts. PATIENTS: Dental casts were retrieved for 71 children (47 boys and 24 girls) at 9 years of age. MAIN OUTCOME MEASURES: GOSLON ratings. RESULTS: Sixty-eight percent of patients had an excellent to satisfactory dental arch relationship (GOSLON Yardstick ratings 1 to 3) at 9 years with a mean rating of 2.85. High caseload surgeons achieved statistically better mean GOSLON ratings than low caseload surgeons (2.72 and 3.33, respectively). CONCLUSIONS: PMH Cleft Unit's dental arch relationship outcomes are comparable to published series of units using similar treatment protocols. High caseload surgeons achieved better dental arch relationships than low caseload surgeons.

Comparing volunteer and professionally collected monitoring data from the rocky subtidal reefs of Southern California, USA.

Volunteer-based citizen monitoring has increasingly become part of the natural resources monitoring framework, but it is often unclear whether the data quality from these programs is sufficient for integration with traditional efforts conducted by professional scientists. At present, the biological and physical characteristics of California's rocky reef kelp forests are concurrently monitored by two such groups, using similar methodologies--underwater visual census (UVC) of fish, benthic invertebrates, and reef habitat, though the volunteer group limits their sampling to transects close to the reef surface and they use a more constrained list of species for enumeration and measurement. Here, we compared the data collected from 13 reefs that were sampled by both programs in 2008. These groups described relatively similar fish communities, total fish abundance and abundance of the dominant fish species but there were some differences in the measured size distributions of the dominant fish species. Descriptions of the benthic invertebrate community were also similar, though there were some differences in relative abundance that may have resulted from the less detailed subsampling protocols used by the volunteers. The biggest difference was in characterization of the physical habitat of the reefs, which appeared to result from selection bias of transect path by the volunteer program towards more complex structured sections of a reef. Changes to address these differences are relatively simple to implement and if so, offer the promise of better integration of the trained volunteer monitoring with that of professional monitoring groups.

A nitrite-oxidising bacterium constitutively consumes atmospheric hydrogen.

Chemolithoautotrophic nitrite-oxidising bacteria (NOB) of the genus Nitrospira contribute to nitrification in diverse natural environments and engineered systems. Nitrospira are thought to be well-adapted to substrate limitation owing to their high affinity for nitrite and capacity to use alternative energy sources. Here, we demonstrate that the canonical nitrite oxidiser Nitrospira moscoviensis oxidises hydrogen (H2) below atmospheric levels using a high-affinity group 2a nickel-iron hydrogenase [Km(app) = 32 nM]. Atmospheric H2 oxidation occurred under both nitrite-replete and nitrite-deplete conditions, suggesting low-potential electrons derived from H2 oxidation promote nitrite-dependent growth and enable survival during nitrite limitation. Proteomic analyses confirmed the hydrogenase was abundant under both conditions and indicated extensive metabolic changes occur to reduce energy expenditure and growth under nitrite-deplete conditions. Thermodynamic modelling revealed that H2 oxidation theoretically generates higher power yield than nitrite oxidation at low substrate concentrations and significantly contributes to growth at elevated nitrite concentrations. Collectively, this study suggests atmospheric H2 oxidation enhances the growth and survival of NOB amid variability of nitrite supply, extends the phenomenon of atmospheric H2 oxidation to an eighth phylum (Nitrospirota), and reveals unexpected new links between the global hydrogen and nitrogen cycles. Long classified as obligate nitrite oxidisers, our findings suggest H2 may primarily support growth and survival of certain NOB in natural environments.

Reaction hijacking of tyrosine tRNA synthetase as a new whole-of-life-cycle antimalarial strategy.

Aminoacyl transfer RNA (tRNA) synthetases (aaRSs) are attractive drug targets, and we present class I and II aaRSs as previously unrecognized targets for adenosine 5'-monophosphate-mimicking nucleoside sulfamates. The target enzyme catalyzes the formation of an inhibitory amino acid-sulfamate conjugate through a reaction-hijacking mechanism. We identified adenosine 5'-sulfamate as a broad-specificity compound that hijacks a range of aaRSs and ML901 as a specific reagent a specific reagent that hijacks a single aaRS in the malaria parasite Plasmodium falciparum, namely tyrosine RS (PfYRS). ML901 exerts whole-life-cycle-killing activity with low nanomolar potency and single-dose efficacy in a mouse model of malaria. X-ray crystallographic studies of plasmodium and human YRSs reveal differential flexibility of a loop over the catalytic site that underpins differential susceptibility to reaction hijacking by ML901.

High Throughput Screening to Identify Selective and Nonpeptidomimetic Proteasome Inhibitors As Antimalarials.

The Ubiquitin Proteasome System is the main proteolytic pathway in eukaryotic cells, playing a role in key cellular processes. The essentiality of the Plasmodium falciparum proteasome is well validated, underlying its potential as an antimalarial target, but selective compounds are required to avoid cytotoxic effects in humans. Almost 550000 compounds were tested for the inhibition of the chymotrypsin-like activity of the P. falciparum proteasome using a Proteasome-GLO luminescence assay. Hits were confirmed in an orthogonal enzyme assay using Rho110-labeled peptides, and selectivity was assessed against the human proteasome. Four nonpeptidomimetic chemical families with some selectivity for the P. falciparum proteasome were identified and characterized in assays of proteasome trypsin and caspase activities and in parasite growth inhibition assays. Target engagement studies were performed, validating our approach. Hits identified are good starting points for the development of new antimalarial drugs and as tools to better understand proteasome function in P. falciparum.

Benthic habitat condition of the continental shelf surrounding oil and gas platforms in the Santa Barbara Channel, Southern California.

The continental shelf of southern California is an important location for the extraction of petroleum and natural gas. Many platforms in the region have been operating for more than four decades and are being targeted for decommissioning. Information on the condition of surrounding habitats to the platforms will be important for regulators. The condition of sediments near (250 m-2 km) four active oil/gas platforms was evaluated with measures of macrobenthic infauna, toxicity, and chemical composition using standardized assessment indices and compared to that of equivalent locations across the region without platforms. Assessment scores indicated that the sediments surrounding the oil platforms were in a relatively good state, with reference-condition infauna, minimal levels of chemical exposure, and five instances (25% of samples) of low-level toxicity. Samples from around the oil platforms were in overall similar condition to the region, with slightly better condition infauna, nearly identical chemistry, and slightly worse toxicity.

A Review of 30 Years of Alveolar Bone Grafting in the Mixed Dentition Using a Standardized Protocol in Western Australia.

BACKGROUND: Outcomes for a continuously applied alveolar bone grafting protocol, established in 1982, are reported and compared to previously published outcomes from the authors' unit and elsewhere. METHODS: A descriptive, retrospective cohort study of alveolar bone grafting outcomes at a tertiary referral cleft center was performed. Records of all alveolar bone grafts between 2002 and 2014 were reviewed (224 grafts). Three-year postoperative periapical radiographs were evaluated using the Bergland, Kindelan, and standardized way to assess graft scores by an external rater. Incomplete records, a syndromic diagnosis, or primary surgery performed elsewhere resulted in 123 grafts being excluded, leaving 101 grafts for assessment. The distribution of scores was compared to the authors' previous studies and international reports. The authors also tested for any impact on the outcome based on cleft type, laterality, timing for incisor or canine eruption, and surgeon experience. RESULTS: A total of 95.6 percent of applicable grafts (66 of 69) were considered "successful" by Bergland scores and 96 percent by Kindelan scores. Eighty-nine percent of grafts were "very good" based on standardized way to assess graft score. No significant differences were detected in outcomes based on timing, cleft type, or laterality. Surgeon experience had a significant impact (p < 0.05) on outcome for Bergland and Kindelan scores. Distribution of Bergland scores did not differ from the authors' earlier studies demonstrating consistent outcomes for over 30 years. CONCLUSIONS: The Western Australian alveolar bone grafting protocol has consistently achieved a very high success rate (96 percent) for over 30 years despite multiple staff changes. These results compared well with best-reported outcomes from worldwide cleft centers. Surgeon training and experience were significant in achieving these outcomes. CLINICAL QUESTION/LEVEL OF EVIDENCE: Therapeutic, IV.

The importance of open science for biological assessment of aquatic environments.

Open science principles that seek to improve science can effectively bridge the gap between researchers and environmental managers. However, widespread adoption has yet to gain traction for the development and application of bioassessment products. At the core of this philosophy is the concept that research should be reproducible and transparent, in addition to having long-term value through effective data preservation and sharing. In this article, we review core open science concepts that have recently been adopted in the ecological sciences and emphasize how adoption can benefit the field of bioassessment for both prescriptive condition assessments and proactive applications that inform environmental management. An example from the state of California demonstrates effective adoption of open science principles through data stewardship, reproducible research, and engagement of stakeholders with multimedia applications. We also discuss technical, sociocultural, and institutional challenges for adopting open science, including practical approaches for overcoming these hurdles in bioassessment applications.

Cellular and Structural Basis of Synthesis of the Unique Intermediate Dehydro-F420-0 in Mycobacteria.

F420 is a low-potential redox cofactor used by diverse bacteria and archaea. In mycobacteria, this cofactor has multiple roles, including adaptation to redox stress, cell wall biosynthesis, and activation of the clinical antitubercular prodrugs pretomanid and delamanid. A recent biochemical study proposed a revised biosynthesis pathway for F420 in mycobacteria; it was suggested that phosphoenolpyruvate served as a metabolic precursor for this pathway, rather than 2-phospholactate as long proposed, but these findings were subsequently challenged. In this work, we combined metabolomic, genetic, and structural analyses to resolve these discrepancies and determine the basis of F420 biosynthesis in mycobacterial cells. We show that, in whole cells of Mycobacterium smegmatis, phosphoenolpyruvate rather than 2-phospholactate stimulates F420 biosynthesis. Analysis of F420 biosynthesis intermediates present in M. smegmatis cells harboring genetic deletions at each step of the biosynthetic pathway confirmed that phosphoenolpyruvate is then used to produce the novel precursor compound dehydro-F420-0. To determine the structural basis of dehydro-F420-0 production, we solved high-resolution crystal structures of the enzyme responsible (FbiA) in apo-, substrate-, and product-bound forms. These data show the essential role of a single divalent cation in coordinating the catalytic precomplex of this enzyme and demonstrate that dehydro-F420-0 synthesis occurs through a direct substrate transfer mechanism. Together, these findings resolve the biosynthetic pathway of F420 in mycobacteria and have significant implications for understanding the emergence of antitubercular prodrug resistance.IMPORTANCE Mycobacteria are major environmental microorganisms and cause many significant diseases, including tuberculosis. Mycobacteria make an unusual vitamin-like compound, F420, and use it to both persist during stress and resist antibiotic treatment. Understanding how mycobacteria make F420 is important, as this process can be targeted to create new drugs to combat infections like tuberculosis. In this study, we show that mycobacteria make F420 in a way that is different from other bacteria. We studied the molecular machinery that mycobacteria use to make F420, determining the chemical mechanism for this process and identifying a novel chemical intermediate. These findings also have clinical relevance, given that two new prodrugs for tuberculosis treatment are activated by F420.

Organic contaminants as an ecological tool to explore niche partitioning: a case study using three pelagic shark species.

Chemical contaminant profiles are linked to an animal's niche, providing a potential tool by which to assess resource partitioning in pelagic species. As proof of concept, we examined contaminant signatures in three species of sharks (Isurus oxyrinchus, Prionace glauca, and Alopias vulpinus) known to overlap in both space and time. Since these sharks comprise a predatory guild within the Southern California Bight (SCB), we predicted that species may partition spatial and dietary resources to limit the extent of competitive exclusion. Indeed, species were distinguishable by both total contaminant loads and their contaminant fingerprint, as random forest analysis found that species could be correctly classified 96% of the time. Our results demonstrate the utility of chemical analyses for ecological studies, and how contaminant tracers can be used in combination with traditional methods to elucidate how species may undergo niche partitioning to reduce competition for overlapping resources within predatory guilds.