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Severe coronavirus disease 2019 (COVID-19) manifests as a life-threatening microvascular syndrome. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses the Spike (S) protein to engage with its receptors and infect host cells. To date, it is still not known whether heart vascular pericytes (PCs) are infected by SARS-CoV-2, and if the S protein alone provokes PC dysfunction. Here, we aimed to investigate the effects of the S protein on primary human cardiac PC signalling and function. Results show, for the first time, that cardiac PCs are not permissive to SARS-CoV-2 infection in vitro, whilst a recombinant S protein alone elicits functional alterations in PCs. This was documented as: (1) increased migration, (2) reduced ability to support endothelial cell (EC) network formation on Matrigel, (3) secretion of pro-inflammatory molecules typically involved in the cytokine storm, and (4) production of pro-apoptotic factors responsible for EC death. Next, adopting a blocking strategy against the S protein receptors angiotensin-converting enzyme 2 (ACE2) and CD147, we discovered that the S protein stimulates the phosphorylation/activation of the extracellular signal-regulated kinase 1/2 (ERK1/2) through the CD147 receptor, but not ACE2, in PCs. The neutralisation of CD147, either using a blocking antibody or mRNA silencing, reduced ERK1/2 activation and rescued PC function in the presence of the S protein. In conclusion, our findings suggest that circulating S protein prompts vascular PC dysfunction, potentially contributing to establishing microvascular injury in organs distant from the site of infection. This mechanism may have clinical and therapeutic implications.Clinical perspectiveSevere COVID-19 manifests as a microvascular syndrome, but whether SARS-CoV-2 infects and damages heart vascular pericytes (PCs) remains unknown.We provide evidence that cardiac PCs are not infected by SARS-CoV-2. Importantly, we show that the recombinant S protein alone elicits cellular signalling through the CD147 receptor in cardiac PCs, thereby inducing cell dysfunction and microvascular disruption in vitro.This study suggests that soluble S protein can potentially propagate damage to organs distant from sites of infection, promoting microvascular injury. Blocking the CD147 receptor in patients may help protect the vasculature not only from infection, but also from the collateral damage caused by the S protein.

Chemokines are secreted proteins that regulate leukocyte migration during inflammatory responses by signaling through chemokine receptors. Full length CC chemokine ligand 14, CCL14(1-74), is a weak agonist for the chemokine receptor CCR1, but its activity is substantially enhanced upon proteolytic cleavage to CCL14(9-74). CCL14 is O-glycosylated at Ser7, adjacent to the site of proteolytic activation. To determine whether glycosylation regulates the activity of CCL14, we used native chemical ligation to prepare four homogeneously glycosylated variants of CCL14(1-74). Each protein was assembled from three synthetic peptide fragments in "one-pot" using two sequential ligation reactions. We show that while glycosylation of CCL14(1-74) did not affect CCR1 binding affinity or potency of activation, sialylated variants of CCL14(1-74) exhibited reduced activity after treatment with plasmin compared to nonsialylated forms. These data indicate that glycosylation may influence the biological activity of CCL14 by regulating its conversion from the full-length to the truncated, activated form.

Background & Aims Despite recent advances in antiviral therapy for hepatitis C virus (HCV), a proportion of patients with genotype 3 (G3) HCV infection do not respond to current all oral treatment regimens. Genomic analyses have identified key polymorphisms correlating with increased resistance to direct-acting antivirals. We previously reported that amino acid polymorphisms (A150V and K206E) in the polymerase (NS5B) of G3 HCV reduce response to sofosbuvir. We now demonstrate that these polymorphisms alter the response to interferon alpha. Methods Quantitative polymerase chain reaction, immunofluorescence, luciferase activity assay, immunoblotting, and flow cytometry were used to study the antiviral effect of interferon (IFN) on DBN G3 HCV-infected cells and G3 HCV replicons. Results We show the presence of the A150V polymorphism markedly reduces the response to IFN alpha (IC50 of S52_WT = 1.162 IU/mL and IC50 of S52_A150V = 14.45 IU/mL, 12.4-fold difference). The induction of IFN-stimulated genes in A150V replicon cells is unaffected, but nuclear localization of active protein kinase R (PKR) is reduced. Blockade of PKR activity reduced the antiviral effect of IFN on wild-type replicons, whereas augmented PKR activation promoted the antiviral effect of IFN on A150V replicons. Furthermore, we show that impaired activation of PKR in A150V replicon cells diminishes cellular apoptosis. Conclusions These results demonstrate that polymorphisms reducing response rates to direct-acting antivirals may function beyond conferring drug resistance by modulating the intrinsic cellular antiviral response.

Tit-for-tat is a familiar principle from animal behavior: individuals respond in kind to being helped or harmed by others. Remarkably some bacteria appear to display tit-for-tat behavior, but how this evolved is not understood. Here we combine evolutionary game theory with agent-based modelling of bacterial tit-for-tat, whereby cells stab rivals with poisoned needles (the type VI secretion system) after being stabbed themselves. Our modelling shows tit-for-tat retaliation is a surprisingly poor evolutionary strategy, because tit-for-tat cells lack the first-strike advantage of preemptive attackers. However, if cells retaliate strongly and fire back multiple times, we find that reciprocation is highly effective. We test our predictions by competing Pseudomonas aeruginosa (a tit-for-tat species) with Vibrio cholerae (random-firing), revealing that P. aeruginosa does indeed fire multiple times per incoming attack. Our work suggests bacterial competition has led to a particular form of reciprocation, where the principle is that of strong retaliation, or ‘tits-for-tat’., Game theory has contributed much to the understanding of social evolution. In an elegant combination of experimental tests and modelling, this study suggests that when bacteria face intense competition, repeated retaliation outcompetes a single tit-for-tat response to attack.

Blood-feeding arthropods produce antiinflammatory salivary proteins called evasins that function through inhibition of chemokine-receptor signaling in the host. Herein, we show that the evasin ACA-01 from theAmblyomma cajennensetick can be posttranslationally sulfated at two tyrosine residues, albeit as a mixture of sulfated variants. Homogenously sulfated variants of the proteins were efficiently assembled via a semisynthetic native chemical ligation strategy. Sulfation significantly improved the binding affinity of ACA-01 for a range of proinflammatory chemokines and enhanced the ability of ACA-01 to inhibit chemokine signaling through cognate receptors. Comparisons of evasin sequences and structural data suggest that tyrosine sulfation serves as a receptor mimetic strategy for recognizing and suppressing the proinflammatory activity of a wide variety of mammalian chemokines. As such, the incorporation of this posttranslational modification (PTM) or mimics thereof into evasins may provide a strategy to optimize tick salivary proteins for antiinflammatory applications.

The first fossil hemipteran from the Late Jurassic of North America, Morrisonnepa jurassica n. gen. et n. sp., is reported and described from the Morrison Formation, Jurassic Salad Bar locality, Sa...

Leukocyte recruitment is a universal feature of tissue inflammation and regulated by the interactions of chemokines with their G protein–coupled receptors. Activation of CC chemokine receptor 2 (CCR2) by its cognate chemokine ligands, including CC chemokine ligand 2 (CCL2), plays a central role in recruitment of monocytes in several inflammatory diseases. In this study, we used phosphoproteomics to conduct an unbiased characterization of the signaling network resulting from CCL2 activation of CCR2. Using data-independent acquisition MS analysis, we quantified both the proteome and phosphoproteome in FlpIn-HEK293T cells stably expressing CCR2 at six time points after activation with CCL2. Differential expression analysis identified 699 significantly regulated phosphorylation sites on 441 proteins. As expected, many of these proteins are known to participate in canonical signal transduction pathways and in the regulation of actin cytoskeleton dynamics, including numerous guanine nucleotide exchange factors and GTPase-activating proteins. Moreover, we identified regulated phosphorylation sites in numerous proteins that function in the nucleus, including several constituents of the nuclear pore complex. The results of this study provide an unprecedented level of detail of CCR2 signaling and identify potential targets for regulation of CCR2 function.

Targeting chemokine signaling is an attractive avenue for the treatment of inflammatory disorders. Tyrosine sulfation is an important post-translational modification (PTM) that enhances chemokine-receptor binding and is also utilized by a number of pathogenic organisms to improve the binding affinity of immune-suppressive chemokine binding proteins (CKBPs). Here we report the display selection of tyrosine-sulfated cyclic peptides using a reprogrammed genetic code to discover high-affinity ligands for the chemokine CCL11 (eotaxin-1). The selected cyclic sulfopeptides possess high affinity for the target chemokine (as well as one or more of the related family members CCL2, CCL7 and CCL24) and inhibit CCL11 activation of CC chemokine receptor 3 (CCR3). This work demonstrates the utility of exploiting native PTMs as binding motifs for the generation of new leads for medicinal chemistry.

The Little Houston Quarry in the Black Hills of Wyoming contains the most diverse vertebrate fauna in the Morrison Formation (Upper Jurassic) north of Como Bluff and the second-most diverse in the entire formation, after Reed’s Quarry 9. The deposit was an occasionally reactivated abandoned river channel, in interbedded green mudstone and laminated green-gray siltstone above a channel sandstone. The dinosaur material is densely distributed and is disarticulated to articulated, with several associated skeletons. The biota contains charophytes, horsetails, a possible seed fern, possible conifers, gastropods, two types of unionoid bivalves, diplostracans (“conchostracans”), a malacostracan, ray-finned fish, lungfish, a frog, salamanders, two types of turtles, rhynchocephalians, a lizard, choristoderes, two types of crocodyliforms, a pterosaur, Allosaurus and several types of small theropods including Tanycolagreus? and probable dromaeosaurids, numerous Camarasaurus and a diplodocine sauropod, a stegosaur, the neornithischian Nanosaurus, and the mammals Docodon, Amblotherium, and a multituberculate. Among these taxa, one of the unionoid bivalves, an atoposaurid crocodyliform, and the species of Amblotherium, which appear to be new and unique to the locality so far. The Docodon material may represent the first occurrence of D. apoxys outside of its type area in Colorado. Additionally, small, unusual theropod tooth types reported here may represent the first Late Jurassic occurrence of cf. Richardoestesia in North America and a possible abelisauroid, respectively.

Trilobites appeared and diversified rapidly in the Cambrian, but it is debated as to whether their radiations and extinctions were globally synchronous or geographically restricted and diachronous. The end of the early Cambrian is a classic example—it has traditionally been defined by the extinction of olenellid and redlichiid trilobites and the appearance of paradoxidid trilobites. Here we integrate the global biostratigraphy of these three trilobite groups with high-precision tuff and tandem detrital zircon U-Pb age constraints to falsify prior models for global synchronicity of these events. For the first time, we demonstrate that olenellid trilobites in Laurentia went extinct at least 3 Ma after the first appearance of paradoxidids in Avalonia and West Gondwana (ca. 509 Ma). They also disappeared before the extinction of redlichiids and prior to the base of the Miaolingian at ca. 506 Ma in South China. This indicates that these three trilobite groups (paradoxidids, olenellids, and redlichiids) and their associated biotas overlapped in time for nearly 40% of Cambrian Epoch 2, Age 4. Implications of this chronological overlap are: (1) trilobite transitions were progressive and geographically mediated rather than globally synchronous; and (2) paleontological databases underestimate the diversity of the early Cambrian. This ∼3 Ma diachroneity, at a critical time in the early evolution of animals, also impacts chemostratigraphic and paleoclimatic data sets that are tied to trilobite biostratigraphy and that collectively underpin our understanding of the Cambrian Earth system.

The MRN complex (MRX in Saccharomyces cerevisiae, made of Mre11, Rad50 and Nbs1/Xrs2) initiates double-stranded DNA break repair and activates the Tel1/ATM kinase in the DNA damage response. Telomeres counter both outcomes at chromosome ends, partly by keeping MRN-ATM in check. We show that MRX is disabled by telomeric protein Rif2 through an N-terminal motif (MIN, MRN/X-inhibitory motif). MIN executes suppression of Tel1, DNA end-resection and non-homologous end joining by binding the Rad50 N-terminal region. Our data suggest that MIN promotes a transition within MRX that is not conductive for endonuclease activity, DNA-end tethering or Tel1 kinase activation, highlighting an Achilles’ heel in MRN, which we propose is also exploited by the RIF2 paralog ORC4 (Origin Recognition Complex 4) in Kluyveromyces lactis and the Schizosaccharomyces pombe telomeric factor Taz1, which is evolutionarily unrelated to Orc4/Rif2. This raises the possibility that analogous mechanisms might be deployed in other eukaryotes as well., Nature Communications, 12 (1), ISSN:2041-1723

Metabarcoding of plant DNA recovered from environmental samples, termed environmental DNA (eDNA), has been used to detect invasive species, track biodiversity changes and reconstruct past ecosystems. The P6 loop of the trnL intron is the most widely utilized gene region for metabarcoding plants due to the short fragment length and subsequent ease of recovery from degraded DNA, which is characteristic of environmental samples. However, the taxonomic resolution for this gene region is limited, often precluding species level identification. Additionally, targeting gene regions using universal primers can bias results as some taxa will amplify more effectively than others. To increase the ability of DNA metabarcoding to better resolve flowering plant species (angiosperms) within environmental samples, and reduce bias in amplification, we developed a multi-gene targeted capture method that simultaneously targets 20 chloroplast gene regions in a single assay across all flowering plant species. Using this approach, we effectively recovered multiple chloroplast gene regions for three species within artificial DNA mixtures down to 0.001 ng/µL of DNA. We tested the detection level of this approach, successfully recovering target genes for 10 flowering plant species. Finally, we applied this approach to sediment samples containing unknown compositions of environmental DNA and confidently detected plant species that were later verified with observation data. Targeting multiple chloroplast gene regions in environmental samples enabled species-level information to be recovered from complex DNA mixtures. Thus, the method developed here, confers an improved level of data on community composition, which can be used to better understand flowering plant assemblages in environmental samples.

We studied plumages and molt patterns of Yellow-bellied (Empidonax flaviventris), Least (E. minimus), and Alder (E. alnorum) flycatchers, primarily on the breeding grounds but with additional data from wintering grounds and a migration stopover site, in order to clarify our knowledge of molt strategies in these species. We determined that these 3 species have a similar overall molt strategy: (1) a partial-to-incomplete preformative molt begun on the breeding grounds, suspended over migration, and completed on the wintering grounds; (2) a limited-to-partial first prealternate molt on the wintering grounds that can overlap the final stages of the preformative molt; (3) a complete definitive prebasic molt begun on summer grounds and completed on wintering grounds; and (4) a limited-to-partial definitive prealternate molt that may overlap with the final stages of the prebasic molt. Our study clarifies previous terminologies and allows these molts to be interpreted in an evolutionary framework. We suggest that observed differences in molt extents among species may be linked to differences in wintering latitude and habitat. The broadleaf forest preferred by Yellow-bellied Flycatcher likely retains insect biomass later into the winter season than the scrub habitat preferred by Least Flycatcher, and this may promote more extensive preformative feather replacement in that species. The much more extensive preformative molt of Alder Flycatcher may be due to its wintering farther south, where there is greater annual solar exposure, perhaps resulting in higher rates of feather degradation. Our data also suggest that the extent of prealternate molt in these species may vary with proximate factors on the winter grounds affecting individuals, rather than body condition at the beginning of winter.

Stargardt disease (STGD1) and ABCA4 retinopathies (ABCA4R) are caused by pathogenic variants in the ABCA4 gene inherited in an autosomal recessive manner. The gene encodes an importer flippase protein that prevents the build-up of vitamin A derivatives that are toxic to the RPE. Diagnosing ABCA4R is complex due to its phenotypic variability and the presence of other inherited retinal dystrophy phenocopies. ABCA4 is a large gene, comprising 50 exons; to date > 2000 variants have been described. These include missense, nonsense, splicing, structural, and deep intronic variants. Missense variants account for the majority of variants in ABCA4. However, in a significant proportion of patients with an ABCA4R phenotype, a second variant in ABCA4 is not identified. This could be due to the presence of yet unknown variants, or hypomorphic alleles being incorrectly classified as benign, or the possibility that the disease is caused by a variant in another gene. This underlines the importance of accurate genetic testing. The pathogenicity of novel variants can be predicted using in silico programs, but these rely on databases that are not ethnically diverse, thus highlighting the need for studies in differing populations. Functional studies in vitro are useful towards assessing protein function but do not directly measure the flippase activity. Obtaining an accurate molecular diagnosis is becoming increasingly more important as targeted therapeutic options become available; these include pharmacological, gene-based, and cell replacement-based therapies. The aim of this review is to provide an update on the current status of genotyping in ABCA4 and the status of the therapeutic approaches being investigated.

In response to infection or injury, the body mounts an inflammatory immune response in order to neutralize pathogens and promote tissue repair. The key effector cells for these responses are the leukocytes (white blood cells), which are specifically recruited to the site of injury. However, dysregulation of the inflammatory response, characterized by the excessive migration of leukocytes to the affected tissues, can also lead to chronic inflammatory diseases. Leukocyte recruitment is regulated by inflammatory mediators, including an important family of small secreted chemokines and their corresponding G protein-coupled receptors expressed in leukocytes. Unsurprisingly, due to their central role in the leukocyte inflammatory response, chemokines and their receptors have been intensely investigated and represent attractive drug targets. Nonetheless, the full therapeutic potential of chemokine receptors has not been realized, largely due to the complexities in the chemokine system. The determination of chemokine-receptor structures in recent years has dramatically shaped our understanding of the molecular mechanisms that underpin chemokine signaling. In this review, we summarize the contemporary structural view of chemokine-receptor recognition, and describe the various binding modes of peptide and small-molecule ligands to chemokine receptors. We also provide some perspectives on the implications of these data for future research and therapeutic development. IMPORTANCE STATEMENT: Given their central role in the leukocyte inflammatory response, chemokines and their receptors are considered as important regulators of physiology and viable therapeutic targets. In this review, we provide a summary of the current understanding of chemokine: chemokine-receptor interactions that have been gained from structural studies, as well as their implications for future drug discovery efforts.

PURPOSE The purpose of this study was to determine if dose de-escalation from 60 to 66 Gy to 30 to 36 Gy of adjuvant radiotherapy (RT) for selected patients with human papillomavirus–associated oropharyngeal squamous cell carcinoma could maintain historical rates for disease control while reducing toxicity and preserving swallow function and quality of life (QOL). PATIENTS AND METHODS MC1273 was a single-arm phase II trial testing an aggressive course of RT de-escalation after surgery. Eligibility criteria included patients with p16-positive oropharyngeal squamous cell carcinoma, smoking history of 10 pack-years or less, and negative margins. Cohort A (intermediate risk) received 30 Gy delivered in 1.5-Gy fractions twice per day over 2 weeks along with 15 mg/m2 docetaxel once per week. Cohort B included patients with extranodal extension who received the same treatment plus a simultaneous integrated boost to nodal levels with extranodal extension to 36 Gy in 1.8-Gy fractions twice per day. The primary end point was locoregional tumor control at 2 years. Secondary end points included 2-year progression-free survival, overall survival, toxicity, swallow function, and patient-reported QOL. RESULTS Accrual was from September 2013 to June 2016 (N = 80; cohort A, n = 37; cohort B, n = 43). Median follow-up was 36 months, with a minimum follow-up of 25 months. The 2-year locoregional tumor control rate was 96.2%, with progression-free survival of 91.1% and overall survival of 98.7%. Rates of grade 3 or worse toxicity at pre-RT and 1 and 2 years post-RT were 2.5%, 0%, and 0%. Swallowing function improved slightly between pre-RT and 12 months post-RT, with one patient requiring temporary feeding tube placement. CONCLUSION Aggressive RT de-escalation resulted in locoregional tumor control rates comparable to historical controls, low toxicity, and little decrement in swallowing function or QOL.

A left mandible of a small crocodyliform found in the Upper Jurassic Morrsion Formation of northeastern Wyoming represents the first occurrence of the atoposaurid Theriosuchus in North America. The specimen demonstrates lower jaw morphology, including heterodonty (as indicated by alveolus shape), similar to Theriosuchus and Knoetschkesuchus, but autapomorphies and a unique combination of characters among these taxa indicate that it is a distinct, new species of Theriosuchus.

Introduction: SARS-CoV-2 antibody detection serves as an important diagnostic marker for past SARS-CoV-2 infection and is essential to determine the spread of COVID-19, monitor potential COVID-19 long-term effects, and to evaluate possible protection from reinfection. A study was conducted across three hospital sites in a large central London NHS Trust in the UK, to evaluate the prevalence and duration of SARS-CoV-2 IgG antibody positivity in healthcare workers.Methods: A matrix equivalence study consisting of 228 participants was undertaken to evaluate the Abbott Panbio™ COVID-19 IgG/IgM rapid test device. Subsequently, 2001 evaluable healthcare workers (HCW), representing a diverse population, were enrolled in a HCW study between June and August 2020. A plasma sample from each HCW was evaluated using the Abbott Panbio™ COVID-19 IgG/IgM rapid test device, with confirmation of IgG-positive results by the Abbott ArchitectTM SARS-CoV-2 IgG assay. 545 participants, of whom 399 were antibody positive at enrolment, were followed up at 3 months.Results: The Panbio™ COVID-19 IgG/IgM rapid test device demonstrated a high concordance with laboratory tests. SARS-CoV-2 antibodies were detected in 506 participants (25.3%) at enrolment, with a higher prevalence in COVID-19 frontline (28.3%) than non-frontline (19.9%) staff. At follow-up, 274/399 antibody positive participants (68.7%) retained antibodies; 4/146 participants negative at enrolment (2.7%) had seroconverted. Non-white ethnicity, older age, hypertension and COVID-19 symptoms were independent predictors of higher antibody levels (OR 1.881, 2.422–3.034, 2.128, and 1.869 respectively), based on Architect™ index quartiles; participants in the first three categories also showed a greater antibody persistence at 3 months.Conclusion: The SARS-CoV-2 anti-nucleocapsid IgG positivity rate among healthcare staff was high, declining by 31.3% during the 3-month follow-up interval. Interestingly, the IgG-positive participants with certain risk factors for severe COVID-19 illness (older age, Black or Asian Ethnicity hypertension) demonstrated greater persistence over time when compared to the IgG-positive participants without these risk factors.

We tested a nootkatone product for insecticide activity against the most prominent vectors of Zika virus (ZIKV), Aedes aegypti, and Aedes albopictus. We tested the permethrin-resistant (PERM-R) Vergel strain of A. aegypti and the permethrin-susceptible (PERM-S) New Orleans strain of A. aegypti to determine if insecticide resistance affected their susceptibility to nootkatone. Bottle bioassays showed that the PERM-S strain (New Orleans) was more susceptible to nootkatone than the confirmed A. aegypti permethrin-resistant (PERM-R) strain, Vergel. The A. albopictus strain ATM-NJ95 was a known PERM-S strain and Coatzacoalcos permethrin susceptibility was unknown but proved to be similar to the ATM-NJ95 PERM-S phenotype. The A. albopictus strains (ATM-NJ95 and Coatzacoalcos) were as susceptible to nootkatone as the New Orleans strain. Bottle bioassays conducted with ZIKV-infected mosquitoes showed that the New Orleans (PERM-S) strain was as susceptible to nootkatone as the mock-infected controls, but the PERM-R strain was less susceptible to nootkatone than the mock-infected controls. Repellency/irritancy and biting inhibition bioassays (RIBB) of A. aegypti determined whether the nootkatone-treated arms of three human subjects prevented uninfected A. aegypti mosquitoes from being attracted to the test subjects and blood-feeding on them. The RIBB analyses data calculated the spatial activity index (SAI) and biting inhibition factor (BI) of A. aegypti at different nootkatone concentrations and then compared the SAI and BI of existing repellency products. We concluded that nootkatone repelled mosquitoes at a rate comparable to 7% DEET or 5% picaridin and has the potential to be an efficacious repellent against adult A. aegypti mosquitoes.

Wastewater-based epidemiology (WBE) was utilized to monitor SARS-CoV-2 RNA in sewage collected from manholes specific to individual student dormitories (dorms) at the University of Arizona in the fall semester of 2020, which led to successful identification and reduction of SARS-CoV-2 transmission events. Positive wastewater samples triggered clinical testing of residents within that dorm; thus, SARS-CoV-2 infected individuals were identified regardless of symptom expression. This current study examined clinical testing data to determine the abundance of asymptomatic versus symptomatic cases in these defined communities. Nasal and nasopharyngeal swab samples processed via antigen and PCR tests indicated that 79.2% of SARS-CoV-2 infections were asymptomatic, and only 20.8% of positive cases reported COVID-19 symptoms at the time of testing. Clinical data was paired with corresponding wastewater virus concentrations, which enabled calculation of viral shedding rates in feces per infected person. Mean shedding rates averaged from positive wastewater samples across all dorms were 7.30 ± 0.67 log10 genome copies per gram of feces (gc/g-feces) based on the N1 gene. Quantification of SARS-CoV-2 fecal shedding rates from infected individuals has been the critical missing component necessary for WBE models to measure and predict SARS-CoV-2 infection prevalence in communities. The findings from this study can be utilized to create models that can be used to inform public health prevention and response actions., Graphical abstract Unlabelled Image

The MRN complex (MRX inSaccharomyces cerevisiae) initiates the repair of DNA double-stranded breaks (DSBs) and activates the Tel1/ATM kinase, which orchestrates the DNA damage response (DDR). Telomeres prevent DDR activation at chromosome ends, partly by keeping MRN-ATM in check. We show that the multiple activities of the MRX complex are disabled by telomeric protein Rif2 through the action of a short motif (MIN,MRN/X-inhibitory motif) at the N-terminal end of the protein. MIN executes telomeric suppression of Tel1, DDR and and non-homologous end joining (NHEJ) via direct biding to the N-terminal region of Rad50. A combination of biochemical and genetic data suggests that Rif2 promotes a transition within the MRX complex that is not conductive for endonuclease activity, DNA-end tethering or Tel1 kinase activation. We suggests that the MIN motif operates in theRIF2paralogORC4(Origin Recognition Complex 4) inK. lactisand in telomeric protein Taz1 inSchizoccharomyces pombe, which is not evolutionarily related to Orc4/Rif2. These results highlight a potential Achilles’ heel in Rad50, the regulatory subunit of MRN, which we suggest has been targeted by different telomeric factors in multiple fungal lineages, raising the possibility that analogous approaches might be deployed in other Eukaryotes as well.

Hallmarks of mature β cells are restricted proliferation and a highly energetic secretory state. Paradoxically, cyclin-dependent kinase 2 (CDK2) is synthesized throughout adulthood, its cytosolic localization raising the likelihood of cell cycle-independent functions. In the absence of any changes in β cell mass, maturity, or proliferation, genetic deletion of Cdk2 in adult β cells enhanced insulin secretion from isolated islets and improved glucose tolerance in vivo. At the single β cell level, CDK2 restricts insulin secretion by increasing KATP conductance, raising the set point for membrane depolarization in response to activation of the phosphoenolpyruvate (PEP) cycle with mitochondrial fuels. In parallel with reduced β cell recruitment, CDK2 restricts oxidative glucose metabolism while promoting glucose-dependent amplification of insulin secretion. This study provides evidence of essential, non-canonical functions of CDK2 in the secretory pathways of quiescent β cells.

Humans and many other hosts establish a diverse community of beneficial microbes anew each generation. The order and identity of incoming symbionts is critical for health, but what determines the success of the assembly process remains poorly understood. Here we develop ecological theory to identify factors important for microbial community assembly. Our method maps out all feasible pathways for the assembly of a given microbiome—with analogies to the mutational maps underlying fitness landscapes in evolutionary biology. Building these “assembly maps” reveals a tradeoff at the heart of the assembly process. Ecological dependencies between members of the microbiota make assembly predictable—and can provide metabolic benefits to the host—but these dependencies may also create barriers to assembly. This effect occurs because interdependent species can fail to establish when each relies on the other to colonize first. We support our predictions with published data from the assembly of the preterm infant microbiota, where we find that ecological dependence is associated with a predictable order of arrival. Our models also suggest that hosts can overcome barriers to assembly via mechanisms that either promote the uptake of multiple symbiont species in one step or feed early colonizers. This predicted importance of host feeding is supported by published data on the impacts of breast milk in the assembly of the human microbiome. We conclude that both microbe to microbe and host to microbe interactions are important for the trajectory of microbiome assembly., Humans and many other hosts establish a diverse community of beneficial microbes anew each generation, but what determines the success of the assembly process remains poorly understood. This study develops ecological theory that reveals the rules underlying the assembly of such host-associated microbiota.

Bacteria often live in diverse communities where the spatial arrangement of strains and species is considered critical for their ecology. However, a test of this hypothesis requires manipulation at the fine scales at which spatial structure naturally occurs. Here we develop a droplet-based printing method to arrange bacterial genotypes across a sub-millimetre array. We print strains of the gut bacterium Escherichia coli that naturally compete with one another using protein toxins. Our experiments reveal that toxin-producing strains largely eliminate susceptible non-producers when genotypes are well-mixed. However, printing strains side-by-side creates an ecological refuge where susceptible strains can persist in large numbers. Moving to competitions between toxin producers reveals that spatial structure can make the difference between one strain winning and mutual destruction. Finally, we print different potential barriers between competing strains to understand how ecological refuges form, which shows that cells closest to a toxin producer mop up the toxin and protect their clonemates. Our work provides a method to generate customised bacterial communities with defined spatial distributions, and reveals that micron-scale changes in these distributions can drive major shifts in ecology., The spatial arrangement of bacterial strains and species within microbial communities is considered crucial for their ecology. Here, Krishna Kumar et al. use a droplet-based printing method to arrange different bacterial genotypes across a sub-millimetre array, and show that micron-scale changes in spatial distributions can drive major shifts in ecology.

Cardiac injury and dysfunction occur in COVID-19 patients and increase the risk of mortality. Causes are ill defined, but could be direct cardiac infection and/or inflammation-induced dysfunction. To identify mechanisms and cardio-protective drugs, we use a state-of-the-art pipeline combining human cardiac organoids with phosphoproteomics and single nuclei RNA sequencing. We identify an inflammatory ‘cytokine-storm’, a cocktail of interferon gamma, interleukin 1β and poly(I:C), induced diastolic dysfunction. Bromodomain-containing protein 4 is activated along with a viral response that is consistent in both human cardiac organoids and hearts of SARS-CoV-2 infected K18-hACE2 mice. Bromodomain and extraterminal family inhibitors (BETi) recover dysfunction in hCO and completely prevent cardiac dysfunction and death in a mouse cytokine-storm model. Additionally, BETi decreases transcription of genes in the viral response, decreases ACE2 expression and reduces SARS-CoV-2 infection of cardiomyocytes. Together, BETi, including the FDA breakthrough designated drug apabetalone, are promising candidates to prevent COVID-19 mediated cardiac damage., A combination of phosphoproteomics, drug screening and single-cell sequencing approaches identifies how cytokines elevated in COVID-19 patients drives cardiac dysfunction, with BET inhibitors serving as potential lead candidates decrease ACE2 cardiac expression and infection.

Physiologically based pharmacokinetic (PBPK) models allow integrated representations of the time course of drug concentrations in the important organs and sites of drug action, toxicity, absorption, metabolism, and excretion. PBPK models have multiple compartments representing defined organs or physiological spaces, with parameters that are potentially directly measurable. They lie on a continuum of pharmacokinetic model types, which includes Compartmental (least complex), Semi-PBPK, PBPK, and Systems Biology (most complex) models. Compartmental models are typically parameterized using a “top-down” approach, where the model is fitted to a specific data set to estimate parameter values. PBPK models are typically parameterized using a “bottom-up” approach, where model parameters are derived from literature, in vitro data, or scaled data from another species. Although there is increasing availability and use of commercial software for PBPK modeling, it is feasible to construct bespoke PBPK for specific projects using general-purpose software platforms. The challenge here is often collecting, collating, and justifying the data used to parameterize the model. In this chapter, the fundamental equations for a simple PBPK models are presented with respect to key “submodels” of an example whole-body model. The current rise in the rate of publication and application of PBPK models is likely to be sustained in the foreseeable future. Contributing factors will likely be the wider use of commercial PBPK models, the advent of broader collective efforts to advance and coordinate PBPK and Systems Biology modeling, and the increasing ease with which bespoke PBPK models can be coded and shared

Olearia pannosa is a plant species listed as vulnerable in Australia. Two subspecies are currently recognised (O. pannosa subsp. pannosa (silver daisy) and O. pannosa subsp. cardiophylla (velvet daisy)), which have overlapping ranges but distinct leaf shape. Remnant populations face threats from habitat fragmentation and climate change. We analysed range-wide genomic data and leaf shape variation to assess population diversity and divergence and to inform conservation management strategies. We detected three distinct genetic groupings and a likely cryptic species. Samples identified as O. pannosa subsp. cardiophylla from the Flinders Ranges in South Australia were genetically distinct from all other samples and likely form a separate, range-restricted species. Remaining samples formed two genetic clusters, which aligned with leaf shape differences but not fully with current subspecies classifications. Levels of genetic diversity and inbreeding differed between the three genetic groups, suggesting each requires a separate management strategy. Additionally, we tested for associations between genetic and environmental variation and carried out habitat suitability modelling for O. pannosa subsp. pannosa populations. We found mean annual maximum temperature explained a significant proportion of genomic variance. Habitat suitability modelling identified mean summer maximum temperature, precipitation seasonality and mean annual rainfall as constraints on the distribution of O. pannosa subsp. pannosa, highlighting increasing aridity as a threat for populations located near suitability thresholds. Our results suggest maximum temperature is an important agent of selection on O. pannosa subsp. pannosa and should be considered in conservation strategies. We recommend taxonomic revision of O. pannosa and provide conservation management recommendations.

Background & aims: Genome-wide association studies in primary biliary cholangitis (PBC) have failed to find X chromosome (chrX) variants associated with the disease. Here, we specifically explore the chrX contribution to PBC, a sexually dimorphic complex autoimmune disease. Methods: We performed a chrX-wide association study, including genotype data from 5 genome-wide association studies (from Italy, United Kingdom, Canada, China, and Japan; 5244 case patients and 11,875 control individuals). Results: Single-marker association analyses found approximately 100 loci displaying P < 5 × 10-4, with the most significant being a signal within the OTUD5 gene (rs3027490; P = 4.80 × 10-6; odds ratio [OR], 1.39; 95% confidence interval [CI], 1.028-1.88; Japanese cohort). Although the transethnic meta-analysis evidenced only a suggestive signal (rs2239452, mapping within the PIM2 gene; OR, 1.17; 95% CI, 1.09-1.26; P = 9.93 × 10-8), the population-specific meta-analysis showed a genome-wide significant locus in East Asian individuals pointing to the same region (rs7059064, mapping within the GRIPAP1 gene; P = 6.2 × 10-9; OR, 1.33; 95% CI, 1.21-1.46). Indeed, rs7059064 tags a unique linkage disequilibrium block including 7 genes: TIMM17B, PQBP1, PIM2, SLC35A2, OTUD5, KCND1, and GRIPAP1, as well as a superenhancer (GH0XJ048933 within OTUD5) targeting all these genes. GH0XJ048933 is also predicted to target FOXP3, the main T-regulatory cell lineage specification factor. Consistently, OTUD5 and FOXP3 RNA levels were up-regulated in PBC case patients (1.75- and 1.64-fold, respectively). Conclusions: This work represents the first comprehensive study, to our knowledge, of the chrX contribution to the genetics of an autoimmune liver disease and shows a novel PBC-related genome-wide significant locus.

In systems as diverse as migrating mammals to road traffic, crowding acts to inhibit efficient collective movement. Bacteria, however, are observed to move in very dense groups containing billions of individuals without causing the gridlock common to other systems. Here we combine experiments, cell tracking and individual-based modelling to study the pathogen Pseudomonas aeruginosa as it collectively migrates across surfaces using grappling-hook like pili. We show that the fast moving cells of a hyperpilated mutant are overtaken and outcompeted by the slower moving wild-type at high cell densities. Using theory developed to study liquid crystals, we demonstrate that this effect is mediated by the physics of topological defects, points where cells with different orientations meet one another. Our analyses reveal that when comet-like defects collide with one another, the fast-moving mutant cells rotate vertically and become trapped. By moving more slowly, wild-type cells avoid this trapping mechanism, allowing them to collectively migrate faster. Our work suggests that the physics of liquid crystals has played a pivotal role in the evolution of collective bacterial motility by exerting a strong selection for cells that exercise restraint in their movement., 48 pages, 4 figures, 10 extended data figures

This review summarises the current state of knowledge regarding the physiology and control of production of thyroid hormones, the effects of chemicals in perturbing their synthesis and release that result in thyroid cancer. It does not consider the potential neurodevelopmental consequences of low thyroid hormones. There are a number of known molecular initiating events (MIEs) that affect thyroid hormone synthesis in mammals and many chemicals are able to activate multiple MIEs simultaneously. AOP analysis of chemical-induced thyroid cancer in rodents has defined the key events that predispose to the development of rodent cancer and many of these will operate in humans under appropriate conditions, if they were exposed to high enough concentrations of the affecting chemicals. There are conditions however that, at the very least, would indicate significant quantitative differences in the sensitivity of humans to these effects, with rodents being considerably more sensitive to thyroid effects by virtue of differences in the biology, transport and control of thyroid hormones in these species as opposed to humans where turnover is appreciably lower and where serum transport of T4/T3 is different to that operating in rodents. There is heated debate around claimed qualitative differences between the rodent and human thyroid physiology, and significant reservations, both scientific and regulatory, still exist in terms of the potential neurodevelopmental consequences of low thyroid hormone levels at critical windows of time. In contrast, the situation for the chemical induction of thyroid cancer, through effects on thyroid hormone production and release, is less ambiguous with both theoretical, and actual data, showing clear dose-related thresholds for the key events predisposing to chemically induced thyroid cancer in rodents. In addition, qualitative differences in transport, and quantitative differences in half life, catabolism and turnover of thyroid hormones, exist that would not operate under normal situations in humans.

The production of in vitro–derived platelets has great potential for transfusion medicine. Here, we build on our experience in the forward programming (FoP) of human pluripotent stem cells (hPSCs) to megakaryocytes (MKs) and address several aspects of the complex challenges to bring this technology to the bedside. We first identify clinical-grade hPSC lines that generate MKs efficiently. We design a bespoke media to maximize both production and maturity of MKs and improve platelet output. Crucially, we transition the lentiviral-based FoP of hPSCs to a nonviral inducible system. We also show how small molecules promote a definitive hematopoiesis phenotype during the differentiation process, thereby increasing the quality of the final product. Finally, we generate platelets using a bioreactor designed to reproduce the physical cues that promote platelet production in the bone marrow. We show that these platelets are able to contribute to both thrombus formation in vitro and have a hemostatic effect in thrombocytopenic mice in vivo.

Cutibacterium (formerly Propionibacterium) acnes (C. acnes) is a commensal bacteria commonly found on the human skin and in the mouth. While the virulence of C. acnes is low in humans, it does produce a biofilm and has been identified as an etiologic agent in a growing number of implant-associated infections. C. acnes infections can prove diagnostically challenging as laboratory cultures can often take greater than 5 days to yield positive results, which are then often disregarded as contaminant. Patients with recurrent bacteremia in the setting of implantable devices warrant further studies to evaluate for an associated valvular or lead endocarditis. The patient in this report demonstrates how cardiac device-related endocarditis secondary to C. acnes can be overlooked due to the indolent nature of this pathogen. This patient presented with an implanted cardiac pacemaker device, as well as retained leads from a prior pacemaker. Transesophageal echocardiography was required to confirm the diagnosis in the setting of multiple positive blood cultures and negative transthoracic echocardiograms over a period of 4 years. The purpose of this report is to highlight the difficulties encountered in diagnosing C. acnes endocarditis in a patient with a cardiac implantable electronic device and persistently positive blood cultures.

The human genome contains ∼29 bitter taste receptors (T2Rs), which are responsible for detecting thousands of bitter ligands, including toxic and aversive compounds. This sentinel function varies between individuals and is underpinned by naturally occurring T2R polymorphisms, which have also been associated with disease. Recent studies have reported the expression of T2Rs and their downstream signaling components within non-gustatory tissues, including the heart. Though the precise role of T2Rs in the heart remains unclear, evidence points toward a role in cardiac contractility and overall vascular tone. In this review, we summarize the extra-oral expression of T2Rs, focusing on evidence for expression in heart; we speculate on the range of potential ligands that may activate them; we define the possible signaling pathways they activate; and we argue that their discovery in heart predicts an, as yet, unappreciated cardiac physiology.

Landbird vital rates, such as productivity and adult survivorship, can be estimated by modeling mist-netting capture data. The proportion in which an adult breeding bird is 1 year of age (a “yearling”), however, has been studied only minimally in a few landbird species. Here we relate yearling proportion to habitat-structure covariates, including reclamation age, in a boreal forest landbird community. Data were collected at 35 constant-effort mist-netting stations over a 6-year period, and consisted of 12,714 captures of adults, of 29 landbird species, including 4,943 captures of yearlings. Accuracy of age determination (yearling or older) was assessed based on recapture data and error rates were estimated at a mean of 8.1% (range 0.0–19.4%) among the 29 species, with 20 species showing age-error rates

Forest insects and pathogens have significant impacts on U.S. forests, annually affecting an area nearly three times that of wildfires and timber harvesting combined. However, coupled with these direct effects of forest insects and pathogens are the indirect impacts through influencing forest management practices, such as harvesting. In an earlier study, we surveyed private woodland owners in the northeastern U.S. and 84% of respondents indicated they intended to harvest in at least one of the presented insect invasion scenarios. This harvest response to insects represents a potentially significant shift in the timing, extent, and species selection of harvesting. Here we used the results from the landowner survey, regional forest inventory data, and characteristics of the emerald ash borer (Species: Agrilus planipennis Fairmaire, 1888) invasion to examine the potential for a rapidly spreading invasive insect to alter harvest regimes and affect regional forest conditions. Our analysis suggests that 25% of the woodland parcels in the Connecticut River Watershed in New England may intend to harvest in response to emerald ash borer. If the emerald ash borer continues to spread at its current rate within the region, and therefore the associated management response occurs in the next decade, this could result in an increase in harvest frequencies, from 2.6% year&minus, 1 (historically) to 3.7% year&minus, 1 through to approximately 2030. If harvest intensities remain at levels found in remeasured Forest Inventory and Analysis plots, this insect-initiated harvesting would result in the removal of 12%&ndash, 13% of the total aboveground biomass. Eighty-one percent of the removed biomass would be from species other than ash, creating a forest disturbance that is over twice the magnitude than that created by emerald ash borer alone, with the most valuable co-occurring species most vulnerable to biomass loss.

The discovery of novel ligands for orphan GPCRs has profoundly affected our understanding of human biology, opening new opportunities for research, and ultimately for therapeutic development. Accordingly, much effort has been directed towards the remaining orphan receptors, yet the rate of GPCR de-orphanisation has slowed in recent years. Here, we briefly review contemporary methodologies of de-orphanisation and then highlight our recent integrated computational and experimental approach for discovery of novel peptide ligands for orphan GPCRs. We identified putative endogenous peptide ligands and found peptide receptor sequence and structural characteristics present in selected orphan receptors. With comprehensive pharmacological screening using three complementary assays, we discovered novel pairings of 17 peptides with five different orphan GPCRs and revealed potential additional ligands for nine peptide GPCRs. These promising findings lay the foundation for future studies on these peptides and receptors to characterise their roles in human physiology and disease.

Background: Severe coronavirus disease 2019 (COVID-19) manifests as a life-threatening microvascular syndrome. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses primarily the capsid spike (S) protein to engage with its receptors and infect host cells. To date, it is still not known if the S protein alone, without the other viral elements, is able to trigger vascular cell signalling and provoke cell dysfunction. Methods: We investigated the effects of the recombinant, stabilised S protein on primary human cardiac pericytes (PCs) signalling and function. Endpoints included cell viability, proliferation, migration, cooperation with endothelial cells (ECs) in angiogenesis assays, and release of pro-inflammatory cytokines. Adopting a blocking strategy against the S protein receptors ACE2 and CD147, we explored which receptor mediates the S protein signalling in PCs. Findings: We show, for the first time, that the recombinant S protein alone elicits functional alterations in cardiac PCs. This was documented as: (1) increased migration, (2) reduced ability to support EC network formation on Matrigel, (3) secretion of pro-inflammatory molecules typically involved in the cytokine storm, and (4) production of pro-apoptotic factors responsible for EC death. Furthermore, the S protein stimulates the phosphorylation/activation of the extracellular signal-regulated kinase 1/2 (ERK1/2) through the CD147 receptor, but not ACE2, in cardiac PCs. Accordingly, the neutralization of CD147, using a blocking antibody, prevented the activation of ERK1/2 and partially rescued the PC function in the presence of the S protein. Interpretation: Our findings suggest the new, intriguing hypothesis that the S protein may elicit vascular cell dysfunction, potentially amplifying, or perpetuating, the damage caused by the whole coronavirus. This mechanism may have clinical and therapeutic implication. Funding: Elizabeth Blackwell Institute (EBI) Rapid Response COVID-19 award. Declaration of Interests: None. Ethics Approval Statement: Ethical approval number 15/LO/1064 from the North Somerset and South Bristol Research Ethics Committee.

The type VI secretion system (T6SS) is a nanomachine used by many bacteria to drive a toxin-laden needle into other bacterial cells. Although the potential to influence bacterial competition is clear, the fitness impacts of wielding a T6SS are not well understood. Here we present a new agent-based model that enables detailed study of the evolutionary costs and benefits of T6SS weaponry during competition with other bacteria. Our model identifies a key problem with the T6SS. Because of its short range, T6SS activity becomes self-limiting, as dead cells accumulate in its way, forming “corpse barriers” that block further attacks. However, further exploration with the model presented a solution to this problem: if injected toxins can quickly lyse target cells in addition to killing them, the T6SS becomes a much more effective weapon. We tested this prediction with single-cell analysis of combat between T6SS-wielding Acinetobacter baylyi and T6SS-sensitive Escherichia coli. As predicted, delivery of lytic toxins is highly effective, whereas nonlytic toxins leave large patches of E. coli alive. We then analyzed hundreds of bacterial species using published genomic data, which suggest that the great majority of T6SS-wielding species do indeed use lytic toxins, indicative of a general principle underlying weapon evolution. Our work suggests that, in the T6SS, bacteria have evolved a disintegration weapon whose effectiveness often rests upon the ability to break up competitors. Understanding the evolutionary function of bacterial weapons can help in the design of probiotics that can both establish well and eliminate problem species., Bacteria attack each other with poison-tipped spears. This study combines theory and experiments to show that these spears (Type VI Secretion Systems) have evolved to break their targets apart with lytic toxins, as this then clears the way to rapidly stab new victims.

Bacteria use complex regulatory networks to cope with stress, but the function of these networks in natural habitats is poorly understood. The competition sensing hypothesis states that bacterial stress response systems can serve to detect ecological competition, but studying regulatory responses in diverse communities is challenging. Here, we solve this problem by using differential fluorescence induction to screen the Salmonella Typhimurium genome for loci that respond, at the single-cell level, to life in biofilms with competing strains of S. Typhimurium and Escherichia coli. This screening reveals the presence of competing strains drives up the expression of genes associated with biofilm matrix production (CsgD pathway), epithelial invasion (SPI1 invasion system), and, finally, chemical efflux and antibiotic tolerance (TolC efflux pump and AadA aminoglycoside 3-adenyltransferase). We validate that these regulatory changes result in the predicted phenotypic changes in biofilm, mammalian cell invasion, and antibiotic tolerance. We further show that these responses arise via activation of major stress responses, providing direct support for the competition sensing hypothesis. Moreover, inactivation of the type VI secretion system (T6SS) of a competitor annuls the responses to competition, indicating that T6SS-derived cell damage activates these stress response systems. Our work shows that bacteria use stress responses to detect and respond to competition in a manner important for major phenotypes, including biofilm formation, virulence, and antibiotic tolerance. ispartof: Current Biology vol:30 issue:7 pages:1231-1244 ispartof: location:England status: published

Our group has previously reported several indolecarboxamides exhibiting potent antitubercular activity. Herein, we rationally designed several arylcarboxamides based on our previously reported homology model and the recently published crystal structure of the mycobacterial membrane protein large 3 (MmpL3). Many analogues showed considerable anti-TB activity against drug-sensitive (DS) Mycobacterium tuberculosis (M. tb) strain. Naphthamide derivatives 13c and 13d were the most active compounds in our study (MIC: 6.55, 7.11 μM, respectively), showing comparable potency to the first line anti-tuberculosis (anti-TB) drug ethambutol (MIC: 4.89 μM). In addition to the naphthamide derivatives, we also identified the quinolone-2-carboxamides and 4-arylthiazole-2-carboxamides as potential MmpL3 inhibitors in which compounds 8i and 18b had MIC values of 9.97 and 9.82 μM, respectively. All four compounds retained their high activity against multidrug-resistant (MDR) and extensively drug-resistant (XDR) M. tb strains. It is worth noting that the two most active compounds 13c and 13d also exhibited the highest selective activity towards DS, MDR and XDR M. tb strains over mammalian cells [IC50 (Vero cells) ≥ 227 μM], indicating their potential lack of cytotoxicity. The four compounds were docked into the MmpL3 active site and were studied for their drug-likeness using Lipinski's rule of five.

Wind disturbance generates heterogeneous microsite structures, including downed logs, windthrow mounds, and pits. While these structures can provide opportunities for regeneration of certain tree species, the long-term influence of microsites and microsite heterogeneity on forest development has not been quantified. We used long-term measurements of a formerly old-growth Tsuga canadensis – Pinus strobus forest severely damaged by a category 3 hurricane in 1938 to quantify the impact of microsite conditions on overstory composition and structure. We asked (i) “What are the patterns in live-tree size, growth, and mortality five and seven decades after disturbance?” and (ii) “What roles do microsite heterogeneity and the presence of disturbance-generated microsites play in long-term forest development following disturbance?” We compared live-tree (>2 cm DBH) development and survival to microsite heterogeneity at the 100 m2 scale. Microsite diversity was positively related to overstory species diversity and stem density and negatively related to average tree size. We propose that plots with higher microsite diversity may have experienced more severe local disturbance, which allowed more species and individuals to establish and created varied niches that allowed these individuals to coexist and generate greater stand-level diversity. These persistent relationships highlight how microsite conditions affect forest development after severe disturbances.

Research conducted in the field identified 14 injury criteria associated with dicamba (Clarity® diglycolamine salt) applied at 0.6 to 280 g ae ha–1(1/1,000 to 1/2 of 560 g ha–1use rate) to indeterminate soybean at V3/V4 or R1/R2. For each criterion, injury was rated using a scale of 0=no injury, 1=slight, 2=slight to moderate, 3=moderate, 4=moderate to severe, and 5=severe. Greatest crop injury 15 d after treatment (DAT) was observed for dicamba rates of 0.6 to 4.4 g ha–1for upper canopy pale leaf margins (3.8 to 4.2) at V3/V4 and for terminal leaf cupping (4.1 to 5.0) at R1/R2, and for rates of 0.6 to 8.8 g ha–1for upper canopy leaf cupping (3.8 to 4.8) and upper canopy leaf surface crinkling (3.4 to 4.4) at V3/V4. Injury 15 DAT was equivalent to the nontreated control for dicamba rates as high as 4.4 g ha–1for lower stem base swelling at V3/V4 and for upper canopy leaf rollover/inversion and terminal leaf necrosis at R1/R2; for rates as high as 8.8 g ha–1for leaf petiole base swelling and stem epinasty at R1/R2, and lower stem base lesions/cracking (V3/V4 and R1/R2 average); and for rates as high as 17.5 g ha–1for lower leaf soil contact at V3/V4 and leaf petiole droop at R1/R2. The response to increasing dicamba rate observed for the injury criteria was in contrast to the steady increase in visual injury and plant height reduction rated as 0 to 100%. The moderate to severe upper canopy leaf cupping, pale leaf margins, and leaf surface crinkling, and terminal leaf cupping 15 DAT with dicamba at 0.6 to 4.4 g ha–1corresponded to soybean yield loss of 1% to 9% for application at V3/V4 and 2% to 17% at R1/R2.

As concerns about sea-level rise mount, municipalities in coastal areas are looking to nature-based protection and adaptation. Oftentimes such projects are marsh creations or restorations, where areas of open water are filled with dredged material to an elevation where emergent vegetation can grow. We are investigating ways biosolids can be used as an amendment to dredged material to enhance project outcomes. Marsh mesocosms were constructed in San Francisco Bay and planted with native cordgrass, Spartina foliosa. Some mesocosms contained a subsurface layer of biosolids. Vegetation grown with biosolids had significantly increased number of new shoots, aboveground biomass, and belowground biomass. Vegetation with only dredged material had greater rooting depths but this result was not significant. By combining natural processes with human infrastructure, the application of biosolids for marsh creation is a sustainable practice.

Disturbance events affect forest composition and structure across a range of spatial and temporal scales, and subsequent forest development may differ after natural, anthropogenic, or compound disturbances. Following large, natural disturbances, salvage logging is a common and often controversial management practice in many regions of the globe. Yet, while the short-term impacts of salvage logging have been studied in many systems, the long-term effects remain unclear. We capitalized on over eighty years of data following an old-growth Tsuga canadensis-Pinus strobus forest in southwestern New Hampshire, USA after the 1938 hurricane, which severely damaged forests across much of New England. To our knowledge, this study provides the longest evaluation of salvage logging impacts, and it highlights developmental trajectories for Tsuga canadensis-Pinus strobus forests under a variety of disturbance histories. Specifically, we examined development from an old-growth condition in 1930 through 2016 across three different disturbance histories: (1) clearcut logging prior to the 1938 hurricane with some subsequent damage by the hurricane (“logged”), (2) severe damage from the 1938 hurricane (“hurricane”), and (3) severe damage from the hurricane followed by salvage logging (“salvaged”). There were no differences in current overstory composition between the different disturbance histories, as most areas shifted strongly away from pre-hurricane composition through nearly complete elimination of P. strobus and corresponding increases in hardwoods (Betula and Acer spp.), while T. canadensis remained dominant. In contrast, eight decades later, structural characteristics remain distinct between logged, hurricane, and salvaged sites. Specifically, trees were larger in the logged and salvaged sites, and pit and mound structures were largest and most abundant in the hurricane site. Tree densities and coarse woody debris biomass was greater in the hurricane site than the logged sites, but not significantly different from salvaged sites. These findings underscore the long-term influence of salvage logging on forest development, indicating convergence in overstory composition over time between logged, salvaged, and non-salvaged areas, but persistent structural differences, especially in microtopographic structures and live tree development. Future salvage logging efforts should consider these impacts and provide a greater range of unsalvaged areas across the landscape to maintain important structural legacies over the long term.

Wave attenuation is a central process in the mechanics of a healthy salt marsh. Understanding how wave attenuation varies with vegetation and hydrodynamic conditions informs models of other marsh processes that are a function of wave energy (e.g. sediment transport) and allows for the incorporation of marshes into coastal protection plans. Here, we examine the evolution of wave height across a tidal salt marsh in San Francisco Bay. Instruments were deployed along a cross-shore transect, starting on the mudflat and crossing through zones dominated by Spartina foliosa and Salicornia pacifica. This dataset is the first to quantify wave attenuation for these vegetation species, which are abundant in the intertidal zone of California estuaries. Measurements were collected in the summer and winter to assess seasonal variation in wave attenuation. Calculated drag coefficients of S. foliosa and S. pacifica were similar, indicating equal amounts of vegetation would lead to similar energy dissipation; however, S. pacifica has much greater biomass close to the bed (

Ecologically dominant species often define ecosystem states, but as human disturbances intensify, their subordinate counterparts increasingly displace them. We consider the duality of disturbance by examining how environmental drivers can simultaneously act as a stressor to dominant species and as a resource to subordinates. Using a model ecosystem, we demonstrate that CO2-driven interactions between species can account for such reversals in dominance; i.e., the displacement of dominants (kelp forests) by subordinates (turf algae). We established that CO2 enrichment had a direct positive effect on productivity of turfs, but a negligible effect on kelp. CO2 enrichment further suppressed the abundance and feeding rate of the primary grazer of turfs (sea urchins), but had an opposite effect on the minor grazer (gastropods). Thus, boosted production of subordinate producers, exacerbated by a net reduction in its consumption by primary grazers, accounts for community change (i.e., turf displacing kelp). Ecosystem collapse, therefore, is more likely when resource enrichment alters competitive dominance of producers, and consumers fail to compensate. By recognizing such duality in the responses of interacting species to disturbance, which may stabilize or exacerbate change, we can begin to understand how intensifying human disturbances determine whether or not ecosystems undergo phase shifts. Refereed/Peer-reviewed

The Mygatt-Moore Quarry is a deposit of several thousand dinosaur bones in the Brushy Basin Member of the Morrison Formation in western Colorado. The site has been worked for more than 30 years and nearly 2400 mapped specimens have been collected. This study gathered data about the quarry from many sources to investigate the origin of the deposit. The Mygatt-Moore Quarry appears to be an attritional deposit of a relatively restricted diversity of dinosaurs, with few other non-dinosaurian taxa, that accumulated in a vernal pool deposit in an overbank setting. Bone modification was mostly by corrosion and breakage by trampling; scavenging was abundant. The paleofauna is dominated by Allosaurus and Apatosaurus (MNI and NIS), with the polacanthid ankylosaur Mymoorapelta less common. The matrix of the main quarry layer includes abundant carbonized fragments of plant material, and the mud during the time of deposition may have been often at least damp and occasionally acidic and dysoxic. The Cleveland-Lloyd Dinosaur Quarry is a close correlate of the Mygatt-Moore Quarry in terms of lithology and taphonomy, but demonstrates significant differences upon close inspection of matrix details and bone modification. Large quarries of fine-grained facies in the Morrison Formation possess a very different preservation mode as well as different taxon and relative abundance profiles from those in coarser sediments, which suggests that more may be learned in the future from taphofacies study of large quarries in mudstone beds.

Nutrient-sensing mechanisms have emerged as the fringe articulating nutritional needs with dietary choices. Carbohydrate, amino acid, fatty acid, mineral, and water-sensing receptors are highly conserved across mammals and birds, consisting of a repertoire of 22 genes known to date. In contrast, bitter receptors are highly divergent and have a high incidence of polymorphisms within and between mammals and birds and are involved in the adaptation of species to specific environments. In addition, the expression of nutrient-sensing genes outside the oral cavity seems to mediate the required decision-making dialogue between the gut and the brain by translating exogenous chemical stimuli into neuronal inputs, and vice versa, to translate the endogenous signals relevant to the nutritional status into specific appetites and the control of feed intake. The relevance of these sensors in nondigestive systems has uncovered fascinating potential as pharmacological targets relevant to respiratory and cardiovascular diseases.