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Ionizing radiation is employed broadly in oncology, but has a narrow therapeutic window arising from nonspecifically induced genomic damage in both healthy and cancerous cells. We employ genome-scale CRISPRi perturb-seq across millions of human cells alongside proliferation screens to profile all expressed genes’ effect on heterogenous cellular responses to ionizing radiation in the human chronic myelogenous leukemia cell line K562. We identify undercharacterized radiation sensitizing genes and leverage rich transcriptomic phenotypes to assign putative functional roles based on clustering. We find perturbations which induce radiation-specific responses in single-cell transcriptomic phenotypes like cell cycle state and chromosomal instability, and show how the stressor environment reveals the role of regulatory programs invisible without radiation. A followup validation perturb-seq experiment was used to determine the replicability and broader applicability of these findings, bolstering our confidence in our generation of high-quality transcriptomic profiles to CRISPRi perturbation and ionizing radiation.

Prion diseases are a group of fatal neurodegenerative disorders characterized by the accumulation of misfolded and aggregated prion protein in the central nervous system. Inhibitory interneuron and synapse loss have been shown to drive hyperexcitability in Alzheimer's disease, epilepsy, schizophrenia, autism, and Rett syndrome. The role of inhibitory interneurons expressing parvalbumin (PV-INs) and somatostatin (SST-INs) in prion diseases remains unclear. This thesis aims to elucidate the role that inhibitory interneurons play in prion disease. Quantification of immunolabeled PV- and SST-INs in a novel knock-in model of prion disease reveals that loss of PV- and SST-INs within the hippocampus and motor cortex is variable and occurs only at terminal disease. Although inhibitory neurons are preserved in a genetic model of prion disease, hippocampal inhibitory synapse perturbations were detectable around post-natal day 20 (P20), in which there is a significant increase in inhibitory VGAT+ synapses. Overall, this study suggests that inhibitory interneuron loss occurs late in disease and is not likely an early driver, but is secondary to earlier changes like neuroinflammation, synapse loss, or other upstream changes in cellular prion protein (PrPC) signaling. Therefore, a comprehensive understanding of the intricate interplay between prion pathology and inhibitory interneuron dysfunction may hold promise for developing targeted therapeutic approaches to dampen aberrant excitatory circuitry and slow the progression of prion disease.

The purposes of this study are (1) to determine whether college students who have taken Biological Sciences Curriculum Study (BSCS) High School Biology attain significantly different grades in college biology courses at the University of Missouri than do college students who have taken a non-BSCS high school biology course, and (2) to determine if first year college students who have had a high school BSCS course possess significantly different attitudes toward college science courses than do non-BSCS high school biology students. Part A of the study analyzed the achievement of 893 Introductory Zoology freshmen. Part B analyzed the achievement of 644 General Botany freshmen. Analysis of covariance, holding scholastic ability constant, was used to determine the relationshi" between high school biology background and college biology achievement. Part C used data on 248 zoology and 165 botany freshmen to test for differences in attitude toward science between students with BSCS and non-BSCS. Results indicated that no significant differences (.05 level) were discernible in achievement in zoology or botany. No differences in attitudes toward science were found between any combination of groups. (BC)

Author proposes that the process of natural selection has resulted in higher forms of life. The Theory of Creation fails to appreciate the continuing nature of the natural selection process. Proofs of the natural selection process and the origin of species with new characteristics are observable. (PS)

Discusses problems of college biology teachers in terms of content choice and student-teacher relationships. Advocates a deemphasis on molecular biology focussing on ecology in general biology courses. Discusses the relative values of interest in students and interest in subject matter, problems of releasing potential for learning, and the nature of authority in student-teacher relationships. (EB)

Most transcriptome-wide association studies (TWASs) so far focus on European ancestry and lack diversity. To overcome this limitation, we aggregated genome-wide association study (GWAS) summary statistics, whole-genome sequences and expression quantitative trait locus (eQTL) data from diverse ancestries. We developed a new approach, TESLA (multi-ancestry integrative study using an optimal linear combination of association statistics), to integrate an eQTL dataset with a multi-ancestry GWAS. By exploiting shared phenotypic effects between ancestries and accommodating potential effect heterogeneities, TESLA improves power over other TWAS methods. When applied to tobacco use phenotypes, TESLA identified 273 new genes, up to 55% more compared with alternative TWAS methods. These hits and subsequent fine mapping using TESLA point to target genes with biological relevance. In silico drug-repurposing analyses highlight several drugs with known efficacy, including dextromethorphan and galantamine, and new drugs such as muscle relaxants that may be repurposed for treating nicotine addiction.

Pest density – plant damage relationships are essential guides for decision-making in integrated pest management. In this article, we established pest density – leaf damage relationships for the beech leaf-mining weevil, Orchestes fagi L. (formerly Rhynchaenus fagi, Coleoptera: Curculionidae), in its invasive range of Nova Scotia, Canada. Outbreaks of O. fagi cause tree-wide leaf necrosis in American beech (Fagus grandifolia Ehrh.), which can eventually result in tree mortality. In 2014 and 2016, we collected weekly samples in stands with American beech and assessed leaves for densities during different life stages (eggs, larvae, and pupae), population proxy measures (adult feeding damage, egg slits, and larval galleries), and percent necrosis. In general, feeding damage and leaf necrosis plateaued soon after the end of budburst, but before the larval mine expanded. This strongly suggested that leaf necrosis may be linked to damage caused by adults or by mine initiation rather than that caused by larval mine expansion and gallery development. The density of O. fagi per leaf for life stages and population proxies all significantly explained ∼42%–81% of the variation in end-of-season percent leaf necrosis. Results from this study provide a variety of relationships that could be used in both short- and long-term monitoring efforts for O. fagi.

Background Malignant peritoneal mesothelioma (MPeM) is clinically distinct and less studied than malignant pleural mesothelioma. We report the genomic and immunophenotypic features of a prospectively collected MPeM cohort. Methods Next-generation sequencing (NGS) was performed on MPeM tumors. Genomic near-haploidization (GNH) was assessed. WT1, BAP1, mesothelin, VISTA, and PD-L1 were examined by immunohistochemistry (IHC) when tissue was available. Overall survival (OS) was stratified by selected genomic and IHC features. Results Fifty consented patients with MPeM (45 epithelioid, 5 non-epithelioid) demonstrated common alterations in BAP1 (60%; 30/50), NF2 (24%; 12/50) SETD2 (22%; 11/50), and TP53 (16%; 8/50). Seventy-six percent (38/50) of specimens were evaluable for allele-specific copy number analysis; 8% (3/38) had GNH. IHC positivity rates were 93% (37/40) for mesothelin, 96% (46/48) for WT1, 50% (19/38) for PD-L1 and 89% (34/38) for VISTA. BAP1 loss by IHC was observed in 76% (29/38), including five wildtype on NGS. Combining NGS and IHC for BAP1, OS was worse with alteration/loss compared to wildtype/retained in all patients (n=37 vs. 13, 43.8 vs. 117.3 months; p=0.04) Three of thirty patients had a pathogenic germline variant: POT1 I78T, MUTYH R109Y, BAP1 E402*. Conclusion MPeM has a distinct biology and genomic composition. CDKN2A/B alterations were rare in MPeM while BAP1, NF2, TP53, SETD2, LATS2 were common. BAP1 alteration/loss was associated with shorter survival when all patients were included. A notable minority of specimens had GNH associated with NF2, TP53, and SETDB1 mutations. Pathogenic germline mutations were found in 3 of 30 patients.

Central adiposity is associated with greater sympathetic support of blood pressure. β-adrenergic receptors (β-AR) buffer sympathetically mediated vasoconstriction and β-AR-mediated vasodilation is attenuated in preclinical models of obesity. With this information, we hypothesized β-AR vasodilation would be lower in obese compared with normal weight adults. Because β-AR vasodilation in normal weight adults is limited by cyclooxygenase (COX) restraint of nitric oxide synthase (NOS), we further explored the contributions of COX and NOS to β-AR vasodilation in this cohort. Forearm blood flow (FBF, Doppler ultrasound) and mean arterial blood pressure (MAP, brachial arterial catheter) were measured and forearm vascular conductance (FVC) was calculated (FVC = FBF/MAP). The rise in FVC from baseline (ΔFVC) was quantified during graded brachial artery infusion of isoproterenol (Iso, 1–12 ng/100 g/min) in normal weight (n = 36) and adults with obesity (n = 22) (18–40 yr old). In a subset of participants, Iso-mediated vasodilation was examined before and during inhibition of NOS [N(G)-monomethyl-l-arginine (l-NMMA)], COX (ketorolac), and NOS + COX (l-NMMA + ketorolac). Iso-mediated increases in FVC did not differ between groups (P = 0.57). l-NMMA attenuated Iso-mediated ΔFVC in normal weight (P = 0.03) but not adults with obesity (P = 0.27). In normal weight adults, ketorolac increased Iso-mediated ΔFVC (P < 0.01) and this response was lost with concurrent l-NMMA (P = 0.67). In contrast, neither ketorolac (P = 0.81) nor ketorolac + l-NMMA (P = 0.40) altered Iso-mediated ΔFVC in adults with obesity. Despite shifts in COX and NOS, β-AR vasodilation is preserved in young adults with obesity. These data highlight the presence of a compensatory shift in microvascular control mechanisms in younger humans with obesity. NEW & NOTEWORTHY We examined β-adrenergic receptor-mediated vasodilation in skeletal muscle of humans with obesity and normal weight. Results show that despite shifts in the contribution of cyclooxygenase and nitric oxide synthase, β-adrenergic-mediated vasodilation is relatively preserved in young, otherwise healthy adults with obesity. These data highlight the presence of subclinical changes in microvascular control mechanisms early in the obesity process and suggest duration of obesity and/or the addition of primary aging may be necessary for overt dysfunction.

The advance of metagenomics in combination with intricate cultivation approaches has facilitated the discovery of novel ammonia-, methane-, and other short-chain alkane-oxidizing microorganisms, indicating that our understanding of the microbial biodiversity within the biogeochemical nitrogen and carbon cycles still is incomplete. The in situ detection and phylogenetic identification of novel ammonia- and alkane-oxidizing bacteria remain challenging due to their naturally low abundances and difficulties in obtaining new isolates from complex samples. Here, we describe an activity-based protein profiling protocol allowing cultivation-independent unveiling of ammonia- and alkane-oxidizing bacteria. In this protocol, 1,7-octadiyne is used as a bifunctional enzyme probe that, in combination with a highly specific alkyne-azide cycloaddition reaction, enables the fluorescent or biotin labeling of cells harboring active ammonia and alkane monooxygenases. Biotinylation of these enzymes in combination with immunogold labeling revealed the subcellular localization of the tagged proteins, which corroborated expected enzyme targets in model strains. In addition, fluorescent labeling of cells harboring active ammonia or alkane monooxygenases provided a direct link of these functional lifestyles to phylogenetic identification when combined with fluorescence in situ hybridization. Furthermore, we show that this activity-based labeling protocol can be successfully coupled with fluorescence-activated cell sorting for the enrichment of nitrifiers and alkane-oxidizing bacteria from complex environmental samples, enabling the recovery of high-quality metagenome-assembled genomes. In conclusion, this study demonstrates a novel, functional tagging technique for the reliable detection, identification, and enrichment of ammonia- and alkane-oxidizing bacteria present in complex microbial communities.

Scientific data 3, 160064 -(2016). doi:10.1038/sdata.2016.64, Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a well-characterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 μm diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 Ångström were recorded. The diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development, the contents of which are described here., Published by Nature Publ. Group, London

The E. coli aminoacyl transferase (AaT) can be used to transfer a variety of unnatural amino acids, including those with azide or alkyne groups, to the α-amine of a protein with an N-terminal Lys or Arg. Subsequent functionalization through either copper-catalyzed or strain-promoted click reactions can be used to label the protein with fluorophores or biotin. This method can be used to directly detect AaT substrates or in a two-step protocol to detect substrates of the mammalian ATE1 transferase.

We test whether vegetation community composition from a 10-year climate manipulation experiment on a Welsh peat bog resembles vegetation communities during periods of climate change inferred from a peat core. Experimentally warmed and combined warmed and droughted treatments drove significant increases in ericaceous shrubs but Sphagnum was unaffected. Similarly, Calluna vulgaris seeds increase during inferred warmer periods in the palaeoecological record. Experimental short-term episodic drought (four 4-week drought treatments) did not affect vegetation. Plant community composition has undergone several abrupt changes throughout the past c. 1500 years, often in response to human disturbance. Only slight changes occurred during the Medieval Climate Anomaly (c. 950-1250 Common Era [CE]) in vegetation and hydrology, while abrupt changes occurred during the Little Ice Age (c. 1300-1850 CE) when water tables were highest, suggesting that these shifts were driven by changes in water table, modulated by climate. A period of water table drawdown c. 1800, synchronous with historical records of increased drainage, corresponds with the development of the present-day vegetation community. Modern analogues for fossil material, characterized by abundant Rhynchospora alba and Sphagnum pulchrum, are more common after this event. Vegetation changes due to climate inferred from the palaeo record differ from those observed in the experiments, possibly relating to differences in the importance of drivers of vegetation change over varying timescales. Whereas temperature is frequently identified as the dominant driver of plant community change in experiments, sustained changes in water table appear to be more important in the long-term record. We find evidence that recent climate change and other anthropogenic stressors (e.g. drainage, heavy metal and nitrogen pollution) may promote the development of novel plant communities without analogues in the fossil record. These communities may be poorer at sequestering carbon and may respond differently to future climate change.Rydym yn aprofi os mae cyfansoddiad cymuned planhigion mewn arbrawf trin hinsawdd o 10 mlynedd ar gors mawn yn Gymru yn debyg i gymunedau oedd yn bodoli yn ystod cyfnodau o newid yn yr hinsawdd, e.e., yr Anomaledd Hinsawdd Canoloesol (AHC - c. 950-1250 CE), a nodwydd o graidd mawn. Fe wnaeth triniaethau arbrofol o cynhesu a cynhesu yn cyfunol efo sychder gyrru cynyddu sylweddol mewn phrysgwydd ericaceous. Doedd na ddim effaith ar digonedd Sphagnum. Yn yr un modd, nath hadau Erica tetralix a Calluna vulgaris cynyddu yn ystod cyfnodau cynhesach a gasglwyd yn y cofnod palaeoecolegol. Ni wnaeth sychder episodig tymor byr arbrofol (pedair triniaeth sychder o 4 wythnos) effeithio cymuned planhigion. Mae cyfansoddiad cymuned planhigion wedi profi sawl newid sydyn trwy gydol y gorffennol c. 1500 flynyddoedd, yn aml mewn ymateb i aflonyddwch dynol. Dim ond newidiadau bach a ddigwyddodd yn ystod yr AHC ar gyfer planhigion a hydroleg, tra digwyddodd newidiadau sydyn yn ystod yr Oes Iâ Fach (tua 1300-1850 CE) pan oedd y trwythiadau dŵr ar eu uchaf, sydd yn awgrymu bod y newidiadau hyn yn cael eu gyrru gan newidiadau yn y lefel trwythiad, wedi'u modiwleiddio gan yr hinsawdd. O gwmpas c.1800 mae yna cyfnod o dynnu i lawr trwythiad dwr, sy'n gydamserol â chofnodion hanesyddol o ddraeniad cynyddol, yn cyfateb i ddatblygiad y gymuned planhygion heddiw. Mae analogau modern ar gyfer deunydd ffosil, a nodweddir gan Rhyncospora alba a Sphagnum pulchrum, yn fwy cyffredin ar ôl y digwyddiad hwn. Mae newidiadau llystyfiant oherwydd hinsawdd a gwelodd yn yr cofnod palaeo yn wahanol i'r rhai a arsylwyd yn yr arbrofion, o bosibl yn ymwneud â gwahaniaethau ym mhwysigrwydd gyrwyr newid llystyfiant dros amserlenni amrywiol. Tra bod tymheredd yn aml yn cael ei nodi fel prif ysgogydd newid cymunedol planhigion mewn arbrofion, mae'n ymddangos bod newidiadau parhaus yn y lefel trwythiad yn bwysicach yn y tymor hir. Mae yna tystiolaeth y gallai newid yn yr hinsawdd yn ddiweddar, efo phwysleisiau anthropogenig eraill (e.e. draenio, llygredd metel trwm a nitrogen) hyrwyddo datblygiad cymunedau planhigion newydd heb analogau yn y cofnod ffosil. Efallai bod y cymunedau hyn yn dlotach wrth atafaelu carbon a gallant ymateb yn wahanol i newid yn yr hinsawdd yn y dyfodol.

Summary Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative condition characterized by the loss of motor neurons. We utilized single-cell transcriptomics to uncover dysfunctional pathways in degenerating motor neurons differentiated from SOD1 E100G ALS patient-derived induced pluripotent stem cells (iPSCs) and respective isogenic controls. Differential gene expression and network analysis identified activation of developmental pathways and core transcriptional factors driving the ALS motor neuron gene dysregulation. Specifically, we identified activation of SMAD2, a downstream mediator of the transforming growth factor β (TGF-β) signaling pathway as a key driver of SOD1 iPSC-derived motor neuron degeneration. Importantly, our analysis indicates that activation of TGFβ signaling may be a common mechanism shared between SOD1, FUS, C9ORF72, VCP, and sporadic ALS motor neurons. Our results demonstrate the utility of single-cell transcriptomics in mapping disease-relevant gene regulatory networks driving neurodegeneration in ALS motor neurons. We find that ALS-associated mutant SOD1 targets transcriptional networks that perturb motor neuron homeostasis., Highlights • Single-cell transcriptomic analysis of SOD1 E100G ALS iPSC-derived motor neurons • Mapping an ALS-relevant transcriptional network • Upregulation of developmental programs in familial and sporadic ALS motor neurons • Inhibition of TGFβ pathway improves SOD1 ALS iPSC-derived motor neuron survival, In this article, Bhinge and colleagues use single-cell transcriptomics to analyze degenerating motor neurons (MNs) differentiated from SOD1 E100G ALS patient-derived iPSCs. Using network analysis, they uncover upregulation of developmental pathways and TGFβ activation in familial and sporadic ALS MNs. Importantly, they find that inhibition of TGFβ signaling leads to improved survival of SOD1 ALS iPSC-derived MNs.

In sweet cherry (Prunus avium), infection by ‘Candidatus Phytoplasma pruni’ results in small fruit with poor color and taste, rendering the fruit unmarketable. Yet the disease pathology is poorly understood, particularly at the cultivar level. Therefore, in this study we examined the physiological effects of Ca. P. pruni infection across a range of cultivars and locations in eastern Washington. We found that infection could be separated into early and established stages based on pathogen titer, which correlated with disease severity, including fruit size, color, and sugar and metabolite content. Furthermore, we observed that the effects of early-stage infections were largely indistinguishable from healthy, uninfected plants. Cultivar- and location-specific disease outcomes were observed with regard to size, color, sugar content, and citric acid content. This study presents the first in-depth assessment of X-disease symptoms and biochemical content of fruit from commercially grown sweet cherry cultivars known to be infected with Ca. P. pruni.

Gefapixant (MK-7264, AF-219), a first-in-class P2X3 antagonist, is being developed as oral treatment for refractory or unexplained chronic cough. Based on in vitro data, gefapixant exerts inhibitory activity on the organic anion transporter (OAT) P1B1 transporter. Therefore, a drug-drug interaction study evaluating the potential effects of gefapixant on the OATP1B1 drug transporter, using pitavastatin as a sensitive probe substrate, was conducted. An open-label, 2-period, fixed-sequence study in 20 healthy adults 18 to 55 years old was conducted. In period 1, a 1-mg oral dose of pitavastatin was administered to each participant. After a ≥4-day washout, in period 2 participants received a 45-mg oral dose of gefapixant twice daily on days 1 through 4. On day 2 of period 2, pitavastatin was coadministered with the morning dose of gefapixant. Pitavastatin exposures following single-dose administration with and without multiple doses of gefapixant were similar: geometric mean ratio (90% confidence interval) of pitavastatin area under the plasma concentration-time curve from time 0 to infinity (AUC0-∞ ) (pitavastatin + gefapixant/pitavastatin alone) was 0.97 (0.93-1.02). The ratio of pitavastatin lactone AUC0-∞ to pitavastatin AUC0-∞ was also comparable between treatments. Administration of gefapixant and pitavastatin was generally well tolerated, with no safety findings of concern. These results support that gefapixant has a low potential to inhibit the OATP1B1 transporter.

In immature oocytes, Balbiani bodies are conserved membraneless condensates implicated in oocyte polarization, the organization of mitochondria, and long-term organelle and RNA storage. In Xenopus laevis, Balbiani body assembly is mediated by the protein Velo1. Velo1 contains an N-terminal prion-like domain (PLD) that is essential for Balbiani body formation. PLDs have emerged as a class of intrinsically disordered regions that can undergo various different types of intracellular phase transitions and are often associated with dynamic, liquid-like condensates. Intriguingly, the Velo1 PLD forms solid-like assemblies. Here we sought to understand why Velo1 phase behavior appears to be biophysically distinct from that of other PLD-containing proteins. Through bioinformatic analysis and coarse-grained simulations, we predict that the clustering of aromatic residues and the amino acid composition of residues between aromatics can influence condensate material properties, organization, and the driving forces for assembly. To test our predictions, we redesigned the Velo1 PLD to test the impact of targeted sequence changes in vivo. We found that the Velo1 design with evenly spaced aromatic residues shows rapid internal dynamics, as probed by fluorescent recovery after photobleaching, even when recruited into Balbiani bodies. Our results suggest that Velo1 might have been selected in evolution for distinctly clustered aromatic residues to maintain the structure of Balbiani bodies in long-lived oocytes. In general, our work identifies several tunable parameters that can be used to augment the condensate material state, offering a road map for the design of synthetic condensates.

Research suggests coaches play a central role in establishing a context conducive to concussion reporting, particularly via direct verbal communication about concussion. Informed by qualitative int...

Determining the diet and trophic status of endangered species can provide insights into their key habitats and predator-prey relationships, both essential for conservation. Integrating dietary information from live-captured and dead-stranded turtles from the same area can also shed light on their ecological diversity. Here, diet intake and prey diversity are determined for juvenile green turtles Chelonia mydas from a mixed stock foraging aggregation in the Southwestern Atlantic Ocean (SWAO) using stable carbon (δ13C) and nitrogen (δ15N) isotope analysis. Skin samples were collected from 117 live-captured (LC) turtles and 66 dead-stranded (DS) individuals along the Paraná coast, southern Brazil. Bayesian isotope ellipse space was determined using the program SIBER. A larger isotopic niche space was found among DS turtles, probably because it included long-term resident turtles and recently settled individuals, the latter of which presented low δ15N values compared to larger putative local turtles. The Bayesian stable isotope mixing model MixSIAR was used to determine dietary contributions, using isotopic values of putative prey. MixSIAR results indicated invertebrates and macroalgae as primary prey groups, showing the omnivorous strategy of green turtles in the SWAO. Moreover, many of the smallest DS turtles had δ15N values suggestive of seagrass consumption, which may reflect individual- and/or life-stage-based diet variability. These findings underscore the value of integrating stranding monitoring protocols with research on live green turtles to evaluate habitat use and diet intake assembled in a neritic foraging area. The data also further knowledge about green turtle foraging ecology and are relevant for species and habitat conservation throughout the SWAO.

Cryptosporidiosis is a leading cause of waterborne diarrheal disease globally and an important contributor to mortality in infants and the immunosuppressed. Despite its importance, the Cryptosporidium community has only had access to a good, but incomplete, Cryptosporidium parvum IOWA reference genome sequence. Incomplete reference sequences hamper annotation, experimental design, and interpretation. We have generated a new C. parvum IOWA genome assembly supported by Pacific Biosciences (PacBio) and Oxford Nanopore long-read technologies and a new comparative and consistent genome annotation for three closely related species: C. parvum, Cryptosporidium hominis, and Cryptosporidium tyzzeri. We made 1926 C. parvum annotation updates based on experimental evidence. They include new transporters, ncRNAs, introns, and altered gene structures. The new assembly and annotation revealed a complete Dnmt2 methylase ortholog. Comparative annotation between C. parvum, C. hominis, and C. tyzzeri revealed that most “missing” orthologs are found, suggesting that the biological differences between the species must result from gene copy number variation, differences in gene regulation, and single-nucleotide variants (SNVs). Using the new assembly and annotation as reference, 190 genes are identified as evolving under positive selection, including many not detected previously. The new C. parvum IOWA reference genome assembly is larger, gap free, and lacks ambiguous bases. This chromosomal assembly recovers all 16 chromosome ends, 13 of which are contiguously assembled. The three remaining chromosome ends are provisionally placed. These ends represent duplication of entire chromosome ends including subtelomeric regions revealing a new level of genome plasticity that will both inform and impact future research.

Primary age-related tauopathy (PART) is a neurodegenerative pathology with features distinct from but also overlapping with Alzheimer disease (AD). While both exhibit Alzheimer-type temporal lobe neurofibrillary degeneration alongside amnestic cognitive impairment, PART develops independently of amyloid-β (Aβ) plaques. The pathogenesis of PART is not known, but evidence suggests an association with genes that promote tau pathology and others that protect from Aβ toxicity. Here, we performed a genetic association study in an autopsy cohort of individuals with PART (n = 647) using Braak neurofibrillary tangle stage as a quantitative trait. We found some significant associations with candidate loci associated with AD (SLC24A4, MS4A6A, HS3ST1) and progressive supranuclear palsy (MAPT and EIF2AK3). Genome-wide association analysis revealed a novel significant association with a single nucleotide polymorphism on chromosome 4 (rs56405341) in a locus containing three genes, including JADE1 which was significantly upregulated in tangle-bearing neurons by single-soma RNA-seq. Immunohistochemical studies using antisera targeting JADE1 protein revealed localization within tau aggregates in autopsy brains with four microtubule-binding domain repeats (4R) isoforms and mixed 3R/4R, but not with 3R exclusively. Co-immunoprecipitation in post-mortem human PART brain tissue revealed a specific binding of JADE1 protein to four repeat tau lacking N-terminal inserts (0N4R). Finally, knockdown of the Drosophila JADE1 homolog rhinoceros (rno) enhanced tau-induced toxicity and apoptosis in vivo in a humanized 0N4R mutant tau knock-in model, as quantified by rough eye phenotype and terminal deoxynucleotidyl transferase dUTP nick end-labeling (TUNEL) in the fly brain. Together, these findings indicate that PART has a genetic architecture that partially overlaps with AD and other tauopathies and suggests a novel role for JADE1 as a modifier of neurofibrillary degeneration.

Avian migration is a spectacular phenomenon, representing the annual movements of billions of birds globally. Because the greatest diversity and numbers of birds migrate at night, opportunities to observe active migration are rare. At a number of localities in North America, however, observers can quantify movements of many typically nocturnal migrants during daylight where they continue after dawn. Such locations have provided much information about species-specific phenology, status, and orientation during migration. Localities where morning flights of land birds can be observed are unevenly distributed, however, and are little reported along the Pacific coast. Here we describe a novel location for the observation of spectacular morning flights of nocturnal migrants during spring migration at Bear Divide, in the western San Gabriel Mountains, Los Angeles County, California. In two years of informal surveys at the site, we have recorded at least one morning with an estimated ~13,500 individual birds passing. Our preliminary analyses suggest that the peak of a species’ migration at Bear Divide is correlated with the latitude of a species’ breeding, being later in the spring as that latitude increases. Our data from Bear Divide provide an independent perspective on migration as quantified by local radar. Further work at this locality may help inform our knowledge of migration phenology and population trends.

A proteomic approach based on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) for protein separation and subsequent mass spectrometry (MS) for protein identification was applied to establish a proteomic reference map for the soybean embryonic axis. Proteins were extracted from dissected embryonic axes and separated in the first dimension using a pH range from 4-7. A total of 401 protein spots were isolated, digested with trypsin, and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). We identified 335 protein spots by searching National Center for Biotechnology Information (NCBI) non redundant databases using the Mascot search engine and found a total of 200 unique proteins. Gene Ontology (GO) analysis was employed to understand the molecular processes in which the identified embryonic axes proteins are involved. The majority of proteins play a functional role in catalytic activity (42.9%) and binding (39.3%), followed by nutrient reservoir activity (5.3%), structural molecular activity (4.0%), antioxidant activity (3.2%), transporter activity (2.4%), enzyme regulator activity (1.2%), molecular transducer activity (0.8%), and transcription regulator activity (0.8%). Our 2D-profiling of soybean axis proteins has established for the first time a baseline proteome on which to investigate and compare factors affecting soybean embryonic development and the interaction of beneficial and pathogenic soilborne organisms during seed germination.

The modern cultivated common bean (Phaseolus vulgaris) has evolved from wild common beans distributed in Central America, Mexico and the Andean region of South America. It has been reported that wild common bean accessions have higher levels of protein content than the domesticated dry bean cultivars. However, there is limited proteomic analysis of wild or domesticated common beans. In this investigation, we reported a proteomic analysis of a wild bean from Mexico. We utilized the TCA/Acetone method for protein extraction, two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) for protein separation, and subsequent mass spectrometry (MS) for protein identification. Proteins were separated in the first dimension using pH range from 4-7. A total of 237 protein spots from the second dimension were isolated, digested with trypsin, and analyzed by MALDI/TOF/TOF mass spectrometry. We identified 141 protein spots by searching NCBI non redundant databases using the Mascot search engine and found a total of 43 unique proteins. Gene Ontology (GO) analysis was employed to understand the molecular processes in which the identified common bean proteins are involved. The majority of proteins are involved in binding (41.5%) and catalytic activity (35.8%), followed by nutrient reservoir activity (7.5%), antioxidant activity (1.9%), transporter activity (3.8%), enzyme regulator activity (3.8%), structural molecule activity (1.9%), and electron carrier activity (3.8%). The results indicate that TCA/Acetone extraction and 2D-PAGE is efficient in separating common bean proteins. Further identification of these proteins by MS demonstrates the quality of this protein extraction method. These results will be useful for the development of value added common beans by alteration of protein components.

Several decades after selenium impacts on wild fish populations were observed in freshwater reservoirs receiving fly ash effluents from electric power facilities at Belews Lake and Hyco Reservoir (North Carolina, USA), developments in selenium (Se) toxicology have led to a greater understanding of Se effects on freshwater fish. These latter advancements have allowed regulatory agencies in several jurisdictions to develop tissue-based toxicity benchmarks for the protection of aquatic life. These benchmarks were generally derived from datasets encompassing multiple fish species and designed to protect the most sensitive species (US Environmental Protection Agency [EPA] water quality criteria). Safety factors have been applied in the development of some Canadian guidelines (British Columbia [BC]), resulting in guidelines that appear to be overly conservative. The present study addresses the question, "Are current tissue-based selenium guidelines and criteria overly protective of freshwater fish populations?" A literature review was conducted of studies in which Se was the primary constituent of concern, to compare tissue concentrations and results of fish population metrics and deformity assessment studies with current regulatory thresholds for the protection of aquatic life in the United States and Canada. EPA fish tissue-based Se criteria were found to be protective of fish populations and, at times, overly protective. Canadian water quality guidelines for Se (BC Ministry of Environment and Climate Change Strategy [BCMOECCS], Environment and Climate Change Canada [ECCC]) were consistently found to be overly protective, especially for benchmarks in which safety factors were used to derive those guidelines. In addition to a synthesis of the results of these studies, various limitations of the reviewed studies are discussed, and recommendations for future studies are proposed. Integr Environ Assess Manag 2022;18:622-630. © 2021 SETAC.

Understanding habitat use and reproductive biology of invasive species is essential to predicting invasions, designing early detection programs, and developing management plans. The rudd (Scardinius erythrophthalmus; Linnaeus, 1758) is an omnivorous fish native to Europe and western Asia that has been translocated to several countries in western Europe, New Zealand, North America, and Africa. However, little is known about early life history of rudd, particularly in invaded ecosystems, limiting our ability to predict invasions and create early detection and control programs. The upper Niagara River has the most abundant population of rudd in North America and has been the focus of several ecological investigations. Our study identified critical nursery habitats by determining which nearshore habitat factors were most strongly associated with presence of age-0 rudd. We found that emergent vegetation was the most important habitat characteristic associated with the presence of age-0 rudd. When emergent vegetation was not present, rudd were more likely to be present at sites with abundant submerged aquatic vegetation. Additionally, the odds of rudd presence decreased as distance to the nearest wetland increased. These findings can be used to create habitat-driven predictive models of rudd invasion and guide early detection programs for rudd outside their native range.

Isoetes jarmaniae sp. nov. is described as a new lycophyte endemic to Tasmania, Australia, where it is confined to peat-bound karstic wetlands in several river valleys in the south-west wilderness. While seemingly morphologically closest to I. drummondii, this quillwort has features that are globally uncommon in Isoetes and unknown in other Australasian taxa. Most notable are its markedly flattened, strongly recurved leaves and disproportionately large sporangium ligules that are more suggestive of South American than Australian taxa. As well, the exceptionally thin and wide (alate) megaspore equatorial ridge is swollen at suture intersections, presenting a slightly triangular shape suggestive of the Indian taxon I. udupiensis. The microspores of I. jarmaniae exhibit exceptionally, perhaps uniquely, fine-papillate ornamentation. An original key placing I. jarmaniae in context with the other Tasmanian Isoetes species is provided. This diminutive, apparently diploid species is evidently maintaining a self-sustaining population within a regionally unique habitat and small geographic range.

Damage to proximal tubules due to exposure to toxicants can lead to conditions such as acute kidney injury (AKI), chronic kidney disease (CKD) and ultimately end‐stage renal failure (ESRF). Studies have shown that kidney proximal epithelial cells can regenerate particularly after acute injury. In the previous study, we utilized an immortalized in vitro model of human renal proximal tubule epithelial cells, RPTEC/TERT1, to isolate HRTPT cell line that co‐expresses stem cell markers CD133 and CD24, and HREC24T cell line that expresses only CD24. HRTPT cells showed most of the key characteristics of stem/progenitor cells; however, HREC24T cells did not show any of these characteristics. The goal of this study was to further characterize and understand the global gene expression differences, upregulated pathways and gene interaction using scRNA‐seq in HRTPT cells. Affymetrix microarray analysis identified common gene sets and pathways specific to HRTPT and HREC24T cells analysed using DAVID, Reactome and Ingenuity software. Gene sets of HRTPT cells, in comparison with publicly available data set for CD133+ infant kidney, urine‐derived renal progenitor cells and human kidney‐derived epithelial proximal tubule cells showed substantial similarity in organization and interactions of the apical membrane. Single‐cell analysis of HRTPT cells identified unique gene clusters associated with CD133 and the 92 common gene sets from three data sets. In conclusion, the gene expression analysis identified a unique gene set for HRTPT cells and narrowed the co‐expressed gene set compared with other human renal–derived cell lines expressing CD133, which may provide deeper understanding in their role as progenitor/stem cells that participate in renal repair.

Participating in sport carries inherent risk of injury. Clinicians execute high-level clinical reasoning and decision making to support athletes to achieve the best outcomes. Accurately diagnosing a problem, estimating prognosis, or selecting the most suitable intervention for each athlete is challenging. Clinical prediction models are tools to assist clinicians in estimating the risk or probability of a health outcome for an individual by using data from multiple predictors. Although common in general medical literature, clinical prediction models are rare in sports medicine. The purpose of this article was to (1) describe the steps required to develop and validate (ie, evaluate) a clinical prediction model for clinical researchers, and (2) help sports medicine clinicians understand and interpret clinical prediction model studies. Using a case study to illustrate how to implement clinical prediction models in practice, we address the following issues in developing and validating a clinical prediction model: study design and data, sample size, missing data, selecting predictors, handling continuous predictors, model fitting, internal and external validation, performance measures, reporting, and model presentation. Our work builds on initiatives to improve diagnostic and prognostic clinical research, including the PROGnosis RESearch Strategy (PROGRESS) series of papers and textbook and the Transparent Reporting of a multivariable prediction model for Individual Prognosis Or Diagnosis (TRIPOD) statement.

Resetting international agricultural governance requires a collective commitment to changing the economic rules of production. This article reports on the challenging questions raised by the Disparity to Parity project, led by a group of farmer-activists, farmer organizations, and scholar-activists in the US. How can parity policies be updated, expanded, redesigned with and for Black, Indigenous, immigrant, cooperative, female and gender diverse farmers and would-be farmers? How does the parity movement join in global solidarity to reset the international agricultural economic and trade rules to reverse the globalization of agriculture that dumps surplus and undermines food sovereignty?

The influence of growing region on hop quality was examined in three American aroma hop varieties (Mosaic®, Simcoe® and Strata®) that were harvested from two to five distinct sites within each of eleven commercial fields located throughout the Willamette Valley, Oregon. Weather, climate, and management data were collected for each of the eleven fields, while site-specific soil characterization was performed at each of the 50 sites. While hop variety had the largest influence on chemical differences, Multiple Factor Analysis revealed regional groupings attributable to differences in soil, weather, and management. Supplemental data for this article is available online at at https://doi.org/10.1080/03610470.2021.1968272 .

The influence of growing region on hop quality is examined in three American aroma hop varieties (Mosaic®, Simcoe® and Strata®) from eleven locations throughout the Willamette Valley, OR. Hops from each site were analyzed for total oil content, α- and β-acids, and the oil was analyzed via GC-FID to quantify selected aroma compounds. Single-field IPAs were brewed using composite samples from each field and assessed via sensory evaluation. While hop variety had the largest influence on chemical differences, as expected, Analysis of Variance revealed differences between fields within the same variety. Sensory discrimination and descriptive testing of the single-field IPAs also showed significant region-based differences among samples within the same variety. Supplemental data for this article is available online at

The mechanics underlying ice–skate friction remain uncertain despite over a century of study. In the 1930s, the theory of self-lubrication from frictional heat supplanted an earlier hypothesis that pressure melting governed skate friction. More recently, researchers have suggested that a layer of abraded wear particles or the presence of quasi-liquid molecular layers on the surface of ice could account for its slipperiness. Here, we assess the dominant hypotheses proposed to govern ice–skate friction and describe experiments conducted in an indoor skating rink aimed to provide observations to test these hypotheses. Our results indicate that the brittle failure of ice under rapid compression plays a strong role. Our observations did not confirm the presence of full-contact water films and are more consistent with the presence of lubricating ice-rich slurries at discontinuous high-pressure zones (HPZs). The presence of ice-rich slurries supporting skates through HPZs merges pressure-melting, abrasion and lubricating films as a unified hypothesis for why skates are so slippery across broad ranges of speeds, temperatures and normal loads. We suggest tribometer experiments to overcome the difficulties of investigating these processes during actual skating trials.

Modern agricultural practices increase the potential for plant pathogen spread, while the advent of affordable whole genome sequencing enables in-depth studies of pathogen movement. Population genomic studies may decipher pathogen movement and population structure as a result of complex agricultural production systems. We used whole genome sequences of 281 Xanthomonas perforans strains collected within one tomato production season across Florida and southern Georgia fields to test for population genetic structure associated with tomato production system variables. We identified six clusters of X. perforans from core gene SNPs that corresponded with phylogenetic lineages. Using whole genome SNPs, we found genetic structure among farms, transplant facilities, cultivars, seed producers, grower operations, regions, and counties. Overall, grower operations that produced their own transplants were associated with genetically distinct and less diverse populations of strains compared to grower operations that received transplants from multiple sources. The degree of genetic differentiation among components of Florida’s tomato production system varied between clusters, suggesting differential dispersal of the strains, such as through seed or contaminated transplants versus local movement within farms. Overall, we showed that the genetic variation of a bacterial plant pathogen is shaped by the structure of the plant production system.

Phytopathogenic Rathayibacter species are unique bacterial plant pathogens because they are obligately vectored by plant parasitic anguinid nematodes to the developing seedheads of forage grasses and cereals. This understudied group of plant-associated Actinomycetes includes the neurotoxigenic plant pathogen R. toxicus, which causes annual ryegrass toxicity in grazing livestock. R. toxicus is currently endemic to Australia and is listed as a plant pathogen select agent by the U.S. Department of Agriculture-Animal and Plant Health Inspection Service. The complex Rathayibacter disease cycle requires intimate interactions with the nematode vector and plant hosts, which warrants an increased understanding of the secretory and surface-associated proteins that mediate these diverse eukaryotic interactions. Here we present the first comparative secretome analysis for this complex, nematode-vectored Rathayibacter genus that compares the three agronomically damaging toxigenic and atoxigenic Rathayibacter species, R. toxicus, R. iranicus, and R. tritici. The exoproteomic comparison identified 1,423 unique proteins between the three species via liquid chromatography-tandem mass spectrometry, leading to the identification of putative pathogenicity-related proteins and proteins that may mediate nematode attachment. Of the uniquely identified proteins, 94 homologous proteins were conserved between the three Rathayibacter exoproteomes and comprised between 43.4 and 58.6% of total protein abundance. Comparative analyses revealed both conserved and uniquely expressed extracellular proteins, which, interestingly, had more similarities to extracellular proteins commonly associated with bacterial animal pathogens than classic plant pathogens. This comparative exoproteome analysis will facilitate the characterization of proteins essential for vector attachment and host colonization and assist in the development of serological diagnostic assays.