Proteomics of SARS-CoV-2-infected host cells reveals therapy targets.

A new coronavirus was recently discovered and named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Infection with SARS-CoV-2 in humans causes coronavirus disease 2019 (COVID-19) and has been rapidly spreading around the globe1,2. SARS-CoV-2 shows some similarities to other coronaviruses; however, treatment options and an understanding of how SARS-CoV-2 infects cells are lacking. Here we identify the host cell pathways that are modulated by SARS-CoV-2 and show that inhibition of these pathways prevents viral replication in human cells. We established a human cell-culture model for infection with a clinical isolate of SARS-CoV-2. Using this cell-culture system, we determined the infection profile of SARS-CoV-2 by translatome3 and proteome proteomics at different times after infection. These analyses revealed that SARS-CoV-2 reshapes central cellular pathways such as translation, splicing, carbon metabolism, protein homeostasis (proteostasis) and nucleic acid metabolism. Small-molecule inhibitors that target these pathways prevented viral replication in cells. Our results reveal the cellular infection profile of SARS-CoV-2 and have enabled the identification of drugs that inhibit viral replication. We anticipate that our results will guide efforts to understand the molecular mechanisms that underlie the modulation of host cells after infection with SARS-CoV-2. Furthermore, our findings provide insights for the development of therapies for the treatment of COVID-19.

Late Cretaceous bird from Madagascar reveals unique development of beaks.

Mesozoic birds display considerable diversity in size, flight adaptations and feather organization1-4, but exhibit relatively conserved patterns of beak shape and development5-7. Although Neornithine (that is, crown group) birds also exhibit constraint on facial development8,9, they have comparatively diverse beak morphologies associated with a range of feeding and behavioural ecologies, in contrast to Mesozoic birds. Here we describe a crow-sized stem bird, Falcatakely forsterae gen. et sp. nov., from the Late Cretaceous epoch of Madagascar that possesses a long and deep rostrum, an expression of beak morphology that was previously unknown among Mesozoic birds and is superficially similar to that of a variety of crown-group birds (for example, toucans). The rostrum of Falcatakely is composed of an expansive edentulous maxilla and a small tooth-bearing premaxilla. Morphometric analyses of individual bony elements and three-dimensional rostrum shape reveal the development of a neornithine-like facial anatomy despite the retention of a maxilla-premaxilla organization that is similar to that of nonavialan theropods. The patterning and increased height of the rostrum in Falcatakely reveals a degree of developmental lability and increased morphological disparity that was previously unknown in early branching avialans. Expression of this phenotype (and presumed ecology) in a stem bird underscores that consolidation to the neornithine-like, premaxilla-dominated rostrum was not an evolutionary prerequisite for beak enlargement.

Skeleton of a Cretaceous mammal from Madagascar reflects long-term insularity.

The fossil record of mammaliaforms (mammals and their closest relatives) of the Mesozoic era from the southern supercontinent Gondwana is far less extensive than that from its northern counterpart, Laurasia1,2. Among Mesozoic mammaliaforms, Gondwanatheria is one of the most poorly known clades, previously represented by only a single cranium and isolated jaws and teeth1-5. As a result, the anatomy, palaeobiology and phylogenetic relationships of gondwanatherians remain unclear. Here we report the discovery of an articulated and very well-preserved skeleton of a gondwanatherian of the latest age (72.1-66 million years ago) of the Cretaceous period from Madagascar that we assign to a new genus and species, Adalatherium hui. To our knowledge, the specimen is the most complete skeleton of a Gondwanan Mesozoic mammaliaform that has been found, and includes the only postcranial material and ascending ramus of the dentary known for any gondwanatherian. A phylogenetic analysis including the new taxon recovers Gondwanatheria as the sister group to Multituberculata. The skeleton, which represents one of the largest of the Gondwanan Mesozoic mammaliaforms, is particularly notable for exhibiting many unique features in combination with features that are convergent on those of therian mammals. This uniqueness is consistent with a lineage history for A. hui of isolation on Madagascar for more than 20 million years.

Functional Divergence in a Multi-gene Family Is a Key Evolutionary Innovation for Anaerobic Growth in Saccharomyces cerevisiae.

The amplification and diversification of genes into large multi-gene families often mark key evolutionary innovations, but this process often creates genetic redundancy that hinders functional investigations. When the model budding yeast Saccharomyces cerevisiae transitions to anaerobic growth conditions, the cell massively induces the expression of seven serine/threonine-rich anaerobically-induced cell wall mannoproteins (anCWMPs): TIP1, TIR1, TIR2, TIR3, TIR4, DAN1, and DAN4. Here, we show that these genes likely derive evolutionarily from a single ancestral anCWMP locus, which was duplicated and translocated to new genomic contexts several times both prior to and following the budding yeast whole genome duplication (WGD) event. Based on synteny and their phylogeny, we separate the anCWMPs into four gene subfamilies. To resolve prior inconclusive genetic investigations of these genes, we constructed a set of combinatorial deletion mutants to determine their contributions toward anaerobic growth in S. cerevisiae. We found that two genes, TIR1 and TIR3, were together necessary and sufficient for the anCWMP contribution to anaerobic growth. Overexpressing either gene alone was insufficient for anaerobic growth, implying that they encode non-overlapping functional roles in the cell during anaerobic growth. We infer from the phylogeny of the anCWMP genes that these two important genes derive from an ancient duplication that predates the WGD event, whereas the TIR1 subfamily experienced gene family amplification after the WGD event. Taken together, the genetic and molecular evidence suggests that one key anCWMP gene duplication event, several auxiliary gene duplication events, and functional divergence underpin the evolution of anaerobic growth in budding yeasts.

The evolution of anaerobic growth in Saccharomycotina yeasts.

Humans rely on the ability of budding yeasts to grow without oxygen in industrial scale fermentations that produce beverages, foods, and biofuels. Oxygen is deeply woven into the energy metabolism and biosynthetic capabilities of budding yeasts. While diverse ecological habitats may provide wide varieties of different carbon and nitrogen sources for yeasts to utilize, there is no direct substitute for molecular oxygen, only a range of availability. Understanding how a small subset of budding yeasts evolved the ability to grow without oxygen could expand the set of useful species in industrial scale fermentations as well as provide insight into the cryptic field of yeast ecology. However, we still do not yet appreciate the full breadth of species that can growth without oxygen, what genes underlie this adaptation, and how these genes have evolved.

Validity Indices of the King-Devick Concussion Test in Hockey Players.

OBJECTIVE: To compare the validity indices of the King-Devick (KD) test in hockey players using any increase in test time over baseline to a 6-second increase as a positive concussion test. We hypothesized the KD test using the 6-second change would yield greater validity indices. DESIGN: Prospective observational cohort study. SETTING: Sports complex. PARTICIPANTS: Sixty-five male hockey players aged 13 to 20 years. INDEPENDENT VARIABLE: Concussion diagnosis. MAIN OUTCOME MEASURES: Time to complete the KD test. Sensitivity (SN), specificity (SP), and the positive likelihood ratios (LRs+) were calculated using 2 thresholds for a positive test: (1) any increase in time and (2) an increase of 6 seconds or greater. RESULTS: Eighteen players (27.7%) were diagnosed with a concussion. Using any increase in time as a positive test yielded the following: SN 72.2%, SP 78.7%, LR+ 3.4, and LR- 0.4. Using the 6-second threshold yielded the following: SN 44.4%, SP 93.6%, LR+ 7.0, and LR- 0.6. A receiver operator curve analysis confirmed 6.40 seconds or greater maximized the LR+. CONCLUSIONS: A 6-second or greater increase in the KD test performance provides greater validity in diagnosing concussion as compared with any increase in performance time.

Crabtree/Warburg-like aerobic xylose fermentation by engineered Saccharomyces cerevisiae.

Bottlenecks in the efficient conversion of xylose into cost-effective biofuels have limited the widespread use of plant lignocellulose as a renewable feedstock. The yeast Saccharomyces cerevisiae ferments glucose into ethanol with such high metabolic flux that it ferments high concentrations of glucose aerobically, a trait called the Crabtree/Warburg Effect. In contrast to glucose, most engineered S. cerevisiae strains do not ferment xylose at economically viable rates and yields, and they require respiration to achieve sufficient xylose metabolic flux and energy return for growth aerobically. Here, we evolved respiration-deficient S. cerevisiae strains that can grow on and ferment xylose to ethanol aerobically, a trait analogous to the Crabtree/Warburg Effect for glucose. Through genome sequence comparisons and directed engineering, we determined that duplications of genes encoding engineered xylose metabolism enzymes, as well as TKL1, a gene encoding a transketolase in the pentose phosphate pathway, were the causative genetic changes for the evolved phenotype. Reengineered duplications of these enzymes, in combination with deletion mutations in HOG1, ISU1, GRE3, and IRA2, increased the rates of aerobic and anaerobic xylose fermentation. Importantly, we found that these genetic modifications function in another genetic background and increase the rate and yield of xylose-to-ethanol conversion in industrially relevant switchgrass hydrolysate, indicating that these specific genetic modifications may enable the sustainable production of industrial biofuels from yeast. We propose a model for how key regulatory mutations prime yeast for aerobic xylose fermentation by lowering the threshold for overflow metabolism, allowing mutations to increase xylose flux and to redirect it into fermentation products.

Benchmarking analysis of computer generated holograms for complex wavefront shaping using pixelated phase modulators.

Wavefront shaping with spatial light modulators (SLMs) enables aberration correction, especially for light control through complex media, like biological tissues and multimode fibres. High-fidelity light field shaping is associated with the calculation of computer generated holograms (CGHs), of which there are a variety of algorithms. The achievable performance of CGH algorithms depends on various parameters. In this paper, four different algorithms for CGHs are presented and compared for complex light field generation. Two iterative, double constraint Gerchberg-Saxton and direct search, and the two analytical, superpixel and phase encoding, algorithms are investigated. For each algorithm, a parameter study is performed varying the modulator's pixel number and phase resolution. The analysis refers to mode field generation in multimode fibre endoscopes and communication. This enables generality by generating specific mode combinations according to certain spatial frequency power spectra. Thus, the algorithms are compared varying spatial frequencies applied to different implementation scenarios. Our results demonstrate that the choice of algorithms has a significant impact on the achievable performance. This comprehensive study provides the required guide for CGH algorithm selection, improving holographic systems towards multimode fibre endoscopy and communications.

Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts.

Secondary metabolites are key in how organisms from all domains of life interact with their environment and each other. The iron-binding molecule pulcherrimin was described a century ago, but the genes responsible for its production in budding yeasts have remained uncharacterized. Here, we used phylogenomic footprinting on 90 genomes across the budding yeast subphylum Saccharomycotina to identify the gene cluster associated with pulcherrimin production. Using targeted gene replacements in Kluyveromyces lactis, we characterized the four genes that make up the cluster, which likely encode two pulcherriminic acid biosynthesis enzymes, a pulcherrimin transporter, and a transcription factor involved in both biosynthesis and transport. The requirement of a functional putative transporter to utilize extracellular pulcherrimin-complexed iron demonstrates that pulcherriminic acid is a siderophore, a chelator that binds iron outside the cell for subsequent uptake. Surprisingly, we identified homologs of the putative transporter and transcription factor genes in multiple yeast genera that lacked the biosynthesis genes and could not make pulcherrimin, including the model yeast Saccharomyces cerevisiae We deleted these previously uncharacterized genes and showed they are also required for pulcherrimin utilization in S. cerevisiae, raising the possibility that other genes of unknown function are linked to secondary metabolism. Phylogenetic analyses of this gene cluster suggest that pulcherrimin biosynthesis and utilization were ancestral to budding yeasts, but the biosynthesis genes and, subsequently, the utilization genes, were lost in many lineages, mirroring other microbial public goods systems that lead to the rise of cheater organisms.

Proceedings From the Ice Hockey Summit III: Action on Concussion.

OBJECTIVES: The Ice Hockey Summit III provided updated scientific evidence on concussions in hockey to inform these 5 objectives: (1) describe sport related concussion (SRC) epidemiology; (2) classify prevention strategies; (3) define objective, diagnostic tests; (4) identify treatment; and (5) integrate science and clinical care into prioritized action plans and policy. METHODS: Our action plan evolved from 40 scientific presentations. The 155 attendees (physicians, athletic trainers, physical therapists, nurses, neuropsychologists, scientists, engineers, coaches, and officials) voted to prioritize these action items in the final Summit session. RESULTS: To (1) establish a national and international hockey database for SRCs at all levels; (2) eliminate body checking in Bantam youth hockey games; (3) expand a behavior modification program (Fair Play) to all youth hockey levels; (4) enforce game ejection penalties for fighting in Junior A and professional hockey leagues; (5) establish objective tests to diagnose concussion at point of care; and (6) mandate baseline testing to improve concussion diagnosis for all age groups. CONCLUSIONS: Expedient implementation of the Summit III prioritized action items is necessary to reduce the risk, severity, and consequences of concussion in the sport of ice hockey.

Qualitative and quantitative evaluation of an interprofessional workshop between physical therapy and medical students.

Interprofessional education (IPE) is an important component of medical education, preparing students for the collaboration necessary for high-quality patient care. This study aimed to compare IPE readiness in pre-qualification physical therapy (PT) and medical (MD) students before and after an interprofessional workshop and identify factors influencing the workshop's perceived educational value. In two consecutive years, students were surveyed with the Readiness for Interprofessional Learning Scale (RIPLS) following a four-hour, case-based workshop. During the second year, students were also surveyed before the workshop and answered open-ended questions about its educational value. PT and MD students had similar mean pre-workshop RIPLS scores (83.0, SD 5.3 vs. 80.7, SD 7.9; p = .27), but post-workshop scores were higher among PT students (86.3, SD 6.5 vs. 80.3, SD 8.8; p < .001). Qualitative thematic analysis of responses to open-ended questions revealed students valued IPE within the workshop. However, MD students in particular identified improvement opportunities in workshop delivery, timing, and content. These factors undermined the perceived educational value for MD students and may have contributed to their lower post-workshop RIPLS scores. This study suggests that a brief workshop can improve readiness for IPE among pre-professional students and highlights the importance of content, delivery, and timing to IPE success.

Randomized, controlled, participant- and rater-blind trial of pharmacogenomic test-guided treatment versus treatment as usual for major depressive disorder.

BACKGROUND: Cohort and cost-effectiveness studies suggest that measuring variation in genes that influence metabolism of common drugs could improve antidepressant treatment outcomes. Prior randomized trials have yielded inconsistent results. METHOD: Multicenter randomized double-blind (subject and rater), controlled trial of pharmacogenomic testing among outpatients with nonpsychotic major depressive disorder. Study participants (n = 304) were randomized 1:1 to assay-guided treatment (AGT; N = 151) or treatment-as-usual (TAU; N = 153). Participants and raters were blinded to study arm; unblinded clinicians received results of a pharmacogenomic test and adjusted treatment in light of the test report. Primary outcome was change over 8 weeks in Hamilton Depression Rating Scale (SIGH-D-17). RESULTS: For the primary comparison of interest, change in SIGH-D-17, no significant difference was detected between AGT and TAU at Week 8 (p = .53). Rates of study completion also did not differ between the arms (AGT 92.7%, TAU 92.2% (χ2 = 0.03, df = 1, p = .86). Exploratory analyses suggested significantly fewer individuals experienced worsening of depressive symptoms following AGT, and that treatment concordant with assay results was associated with greater likelihood of remission. CONCLUSION: Pharmacogenomic testing using a panel of pharmacokinetic and pharmacodynamic variants was not associated with significant improvement in the primary efficacy outcome when providers were unconstrained by the assay results. Further investigation is needed to understand the discordance with cost-effectiveness results and among randomized trials.

First cranial remains of a gondwanatherian mammal reveal remarkable mosaicism.

Previously known only from isolated teeth and lower jaw fragments recovered from the Cretaceous and Palaeogene of the Southern Hemisphere, the Gondwanatheria constitute the most poorly known of all major mammaliaform radiations. Here we report the discovery of the first skull material of a gondwanatherian, a complete and well-preserved cranium from Upper Cretaceous strata in Madagascar that we assign to a new genus and species. Phylogenetic analysis strongly supports its placement within Gondwanatheria, which are recognized as monophyletic and closely related to multituberculates, an evolutionarily successful clade of Mesozoic mammals known almost exclusively from the Northern Hemisphere. The new taxon is the largest known mammaliaform from the Mesozoic of Gondwana. Its craniofacial anatomy reveals that it was herbivorous, large-eyed and agile, with well-developed high-frequency hearing and a keen sense of smell. The cranium exhibits a mosaic of primitive and derived features, the disparity of which is extreme and probably reflective of a long evolutionary history in geographic isolation.

Proceedings from the Ice Hockey Summit III: Action on Concussion.

The Ice Hockey Summit III provided updated scientific evidence on concussions in hockey to inform these five objectives: 1) describe sport-related concussion (SRC) epidemiology, 2) classify prevention strategies, 3) define objective, diagnostic tests, 4) identify treatment, and 5) integrate science and clinical care into prioritized action plans and policy. Our action plan evolved from 40 scientific presentations. The 155 attendees (physicians, athletic trainers, physical therapists, nurses, neuropsychologists, scientists, engineers, coaches, and officials) voted to prioritize these action items in the final Summit session. 1) Establish a national and international hockey data base for SRC at all levels, 2) eliminate body checking in Bantam youth hockey games, 3) expand a behavior modification program (Fair Play) to all youth hockey levels, 4) enforce game ejection penalties for fighting in Junior A and professional hockey leagues, 5) establish objective tests to diagnose concussion at point of care (POC), and 6) mandate baseline testing to improve concussion diagnosis for all age groups. Expedient implementation of the Summit III prioritized action items is necessary to reduce the risk, severity, and consequences of concussion in the sport of ice hockey.

Real-time superchannel transmission over 10,500 km submarine link at 4.66 b/s/Hz spectral efficiency.

We show real-time measurement of error-free superchannel transmission over more than 10,500 km of large-area fiber at a spectral efficiency of 4.66 b/s/Hz, utilizing subcarrier based signal processing optimized at 5.4 GBd.

Influence of Neck Laceration Protectors on Cervical Range of Motion.

OBJECTIVE: To examine the effect of a hockey neck laceration protector (NLP) on cervical range of motion (ROM) along with the athlete's perception on comfort and restrictiveness. Our hypothesis was that all styles of NLPs would limit cervical ROM compared to no NLP, and that certain designs of NLPs would be perceived as more restrictive and less comfortable. DESIGN: Cross-sectional observational analytic. SETTING: Outpatient sports medicine clinic. PARTICIPANTS: Forty-six male and female high school hockey players (age 14-18). INDEPENDENT VARIABLES: Four commercially available NLPs and no NLP. MAIN OUTCOME MEASURES: Cervical ROM and participant feedback regarding restrictiveness and comfort. RESULTS: ROM values while wearing any of the NLPs were significantly less than no NLP for all cervical motion measurements (P < 0.05) with the exception of the Bauer Premium NLP for left rotation (P = 0.792). Significant differences were found between the 4 NLPs in terms of perceived restrictiveness and comfort (P < 0.05). CONCLUSIONS: NLPs may reduce the risk of a neck laceration, but appear to have a negative impact on cervical ROM. This study challenges manufactures to design NLPs that cover vulnerable neck anatomy but do not limit a player's ROM. NLP designs that are most comfortable and least restrictive are recommended.

Concussion in Ice Hockey: Current Gaps and Future Directions in an Objective Diagnosis.

OBJECTIVE: This review provides an update on sport-related concussion (SRC) in ice hockey and makes a case for changes in clinical concussion evaluation. Standard practice should require that concussions be objectively diagnosed and provide quantitative measures of the concussion injury that will serve as a platform for future evidence-based treatment. METHODS: The literature was surveyed to address several concussion-related topics: research in ice hockey-related head trauma, current subjective diagnosis, promising components of an objective diagnosis, and current and potential treatments. MAIN RESULTS: Sport-related head trauma has marked physiologic, pathologic, and psychological consequences for athletes. Although animal models have been used to simulate head trauma for pharmacologic testing, the current diagnosis and subsequent treatment in athletes still rely on an athlete's motivation to report or deny symptoms. Bias-free, objective diagnostic measures are needed to guide quantification of concussion severity and assessment of treatment effects. Most of the knowledge and management guidelines of concussion in ice hockey are generalizable to other contact sports. CONCLUSIONS: There is a need for an objective diagnosis of SRC that will quantify severity, establish a prognosis, and provide effective evidence-based treatment. Potential methods to improve concussion diagnosis by health care providers include a standardized concussion survey, the King-Devick test, a quantified electroencephalogram, and blood analysis for brain cell-specific biomarkers.

Inferring Speciation Processes from Patterns of Natural Variation in Microbial Genomes.

Microbial species concepts have long been the focus of contentious debate, fueled by technological limitations to the genetic resolution of species, by the daunting task of investigating phenotypic variation among individual microscopic organisms, and by a lack of understanding of gene flow in reproductively asexual organisms that are prone to promiscuous horizontal gene transfer. Population genomics, the emerging approach of analyzing the complete genomes of a multitude of closely related organisms, is poised to overcome these limitations by providing a window into patterns of genome variation revealing the evolutionary processes through which species diverge. This new approach is more than just an extension of previous multilocus sequencing technologies, in that it provides a comprehensive view of interacting evolutionary processes. Here we argue that the application of population genomic tools in a rigorous population genetic framework will help to identify the processes of microbial speciation and ultimately lead to a general species concept based on the unique biology and ecology of microorganisms.

Ubiquitin-like small archaeal modifier proteins (SAMPs) in Haloferax volcanii.

Archaea, one of three major evolutionary lineages of life, encode proteasomes highly related to those of eukaryotes. In contrast, archaeal ubiquitin-like proteins are less conserved and not known to function in protein conjugation. This has complicated our understanding of the origins of ubiquitination and its connection to proteasomes. Here we report two small archaeal modifier proteins, SAMP1 and SAMP2, with a beta-grasp fold and carboxy-terminal diglycine motif similar to ubiquitin, that form protein conjugates in the archaeon Haloferax volcanii. The levels of SAMP-conjugates were altered by nitrogen-limitation and proteasomal gene knockout and spanned various functions including components of the Urm1 pathway. LC-MS/MS-based collision-induced dissociation demonstrated isopeptide bonds between the C-terminal glycine of SAMP2 and the epsilon-amino group of lysines from a number of protein targets and Lys 58 of SAMP2 itself, revealing poly-SAMP chains. The widespread distribution and diversity of pathways modified by SAMPylation suggest that this type of protein conjugation is central to the archaeal lineage.