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As one of the key components in model‐informed drug discovery and development, physiologically‐based pharmacokinetic (PBPK) modeling linked with in vitro‐to‐in vivo extrapolation (IVIVE) is widely applied to quantitatively predict drug–drug interactions (DDIs) on drug‐metabolizing enzymes and transporters. This study aimed to investigate an IVIVE for intestinal P‐glycoprotein (Pgp, ABCB1)‐mediated DDIs among three Pgp substrates, digoxin, dabigatran etexilate, and quinidine, and two Pgp inhibitors, itraconazole and verapamil, via PBPK modeling. For Pgp substrates, assuming unbound Michaelis‐Menten constant (K m) to be intrinsic, in vitro‐to‐in vivo scaling factors for maximal Pgp‐mediated efflux rate (J max) were optimized based on the clinically observed results without co‐administration of Pgp inhibitors. For Pgp inhibitors, PBPK models utilized the reported in vitro values of Pgp inhibition constants (K i), 1.0 μM for itraconazole and 2.0 μM for verapamil. Overall, the PBPK modeling sufficiently described Pgp‐mediated DDIs between these substrates and inhibitors with the prediction errors of less than or equal to ±25% in most cases, suggesting a reasonable IVIVE for Pgp kinetics in the clinical DDI results. The modeling results also suggest that Pgp kinetic parameters of both the substrates (K m and J max) and the inhibitors (K i) are sensitive to Pgp‐mediated DDIs, thus being key for successful DDI prediction. It would also be critical to incorporate appropriate unbound inhibitor concentrations at the site of action into PBPK models. The present results support a quantitative prediction of Pgp‐mediated DDIs using in vitro parameters, which will significantly increase the value of in vitro studies to design and run clinical DDI studies safely and effectively.

Background & Aims: Intestinal stem cells (ISCs) are sensitive to dietary alterations and nutrient availability. Neurotensin (NT), a gut peptide localized predominantly to the small bowel and released by fat ingestion, stimulates the growth of intestinal mucosa under basal conditions and during periods of nutrient deprivation, suggesting a possible role for NT on ISC function. Methods: Leucine-rich repeat-containing G-protein coupled receptor 5-Enhanced Green Fluorescent Protein (Lgr5-EGFP) NT wild type (Nt+/+) and Lgr5-EGFP NT knockout (Nt-/-) mice were fed ad libitum or fasted for 48 hours. Small intestine tissue and crypts were examined by gene expression analyses, fluorescence-activated cell sorting, Western blot, immunohistochemistry, and crypt-derived organoid culture. Drosophila expressing NT in midgut enteroendocrine cells were fed a standard diet or low-energy diet and esg-green fluorescent protein+ ISCs were quantified via immunofluorescence. Results: Loss of NT impaired crypt cell proliferation and ISC function in a manner dependent on nutrient status. Under nutrient-rich conditions, NT stimulated extracellular signal-regulated kinases 1 and 2 signaling and the expression of genes that promote cell-cycle progression, leading to crypt cell proliferation. Under conditions of nutrient depletion, NT stimulated WNT/β-catenin signaling and promoted an ISC gene signature, leading to enhanced ISC function. NT was required for the induction of WNT/β-catenin signaling and ISC-specific gene expression during nutrient depletion, and loss of NT reduced crypt cell proliferation and impaired ISC function and Lgr5 expression in the intestine during fasting. Conversely, the expression of NT in midgut enteroendocrine cells of Drosophila prevented loss of ISCs during nutrient depletion. Conclusions: Collectively, our findings establish an evolutionarily conserved role for NT in ISC maintenance during nutritional stress. GSE182828

Brain research has in recent years indisputably entered a new epoch, driven bysubstantialmethodologicaladvances and digitallyenabled data integration and modeling at multiple scales –from molecules to the whole system. Major advances are emerging at theintersection of neurosciencewith technology and computing. This new science of the brain integrates high-quality basic research,systematic data integration across multiple scales, a new culture of large-scale collaboration andtranslation into applications. A systematic approach, as pioneered in Europe’s Human Brain Project(HBP), will be essential in meeting the pressing medical andtechnological challenges of the comingdecade. The aims of this paper are To develop a concept for the coming decade of digital brain research To discuss it with the research community at large, with the aim of identifying points of convergence and common goals To provide a scientific framework for current and future development of EBRAINS To inform and engage stakeholders, funding organizations and research institutions regarding future digital brain research To identify and address key ethical and societal issues While we do not claim that there is a ‘one size fits all’ approach to addressing these aspects, we areconvinced that discussions around the theme of digital brain research will help drive progress in thebroader field of neuroscience. You can submit your comments here and be considered for co-authorship Or become a supporter by clicking here More information below Comments on this manuscript are welcome This manuscriptis a living document that is being further developed in a participatory process. The work has been initiated by the Science and Infrastructure Board of the Human Brain Project (HBP). Now, the entire research community is invited to contribute to shaping the vision by submitting comments.Comments can be submitted via an online commentary form here. All submitted comments will be considered and discussed. The final decision on whether edits or additions will be made to the next version of the manuscript based on an individual comment will be made by the Science and Infrastructure Board (SIB) of the Human Brain Project (HBP) at regular intervals. The final version of the manuscript will be prepared and published in the next months. Comments may be submitted until the end of May, 2023. Every researcher is welcome to provide comment or indicate support for the contents of this paper and jointly shape the future of brain research. Supporters of the paper: Pietro Avanzini, Marc Beyer, Maria Del Vecchio, Jitka Annen, Maurizio Mattia, Steven Laureys, Rosanne Edelenbosch, Rafael Yuste, Jean-Pierre Changeux, Linda Richards, Hye Weon Jessica Kim, Chrysoula Samara, Luis Miguel González de la Garza, Nikoleta Petalidou, Vasudha Kulkarni, Cesar David Rincon, Isabella O'Shea, Munira Tamim Electricwala, Nicola Palomero-Gallagher, Bernd Carsten Stahl, Bahar Hazal Yalcinkaya, Meysam Hashemi, Carola Sales Carbonell, Marcel Carrère, Anthony Randal McIntosh, Hiba Sheheitli, Abolfazl Ziaeemehr, Martin Breyton, Giovanna Ramos Queda, Anirudh NIhalani Vattikonda, Gyorgy Buzsaki George Ogoh, William Knight Torbjørn V Ness, MIchiel van der Vlag, Mu-ming Poo.

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.

Rationale: Fetal growth and survival depend critically on proper development and integrity of the vascular system. Fli1 (Friend leukemia integration 1), a member of the Ets family of transcription factors, plays critical roles in vascular morphogenesis and homeostasis at mid-gestation, the developmental stage at which expression of its upstream regulator, Etv2, ceases. However, molecular mechanisms of Fli1 action in vascular morphogenesis remain incompletely understood. Objective: To dissect molecular mechanisms of vascular morphogenesis governed by Fli1. Methods and Results: Utilizing Fli1 promoter-driven lineage-specific LacZ expression, Fli1 loss-of-function strategies, and a series of molecular techniques, we demonstrate that Fli1 expression in multipotent myogenic progenitor cells (MPCs) occurs independent of Etv2, and loss of Fli1 expression results in a significant increase in LacZ + cells in mesoderm within somites and limb buds, leading to reciprocal regulation of the expression of several key endothelial and myogenic genes and vascular abnormalities. Conversely, embryos harboring conditional Fli1 gain-of-function in MPCs manifested aberrant vasculogenesis with lack of myogenesis. Mechanistically, elevated Fli1 activity in myoblasts and in adult MPCs (also called satellite cells) of X-linked muscular dystrophic mdx mice markedly induced endothelial, but attenuated myogenic, gene expression and differentiation. Importantly, ectopic expression of Myf5 or MyoD, two key myogenic regulators, in Fli1-expressing myoblasts restored their differentiation potential, indicating that levels of Fli1 and myogenic regulators in MPCs inversely regulate their endothelial versus myogenic potential. Conclusions: Fli1 governs vascular morphogenesis by regulating endothelial potential by inversely regulating endothelial versus myogenic programs in MPCs. Our data uncover an important and previously unrecognized mechanism of vascular morphogenesis governed by Fli1 and highlight the physiological significance of the fine tuning of Fli1 activity in multipotent progenitors for proper vascular and muscle morphogenesis during development and disease.

Phloem loading and transport are fundamental processes for allocating carbon from source organs to sink tissues. Cotton (Gossypium spp.) has a high sink demand for the cellulosic fibers that grow on the seed coat and for the storage reserves in the developing embryo, along with the demands of new growth in the shoots and roots. Addressing how cotton mobilizes resources from source leaves to sink organs provides insight into processes contributing to fiber and seed yield. Plasmodesmata frequencies between companion cells and flanking parenchyma in minor veins are higher than expected for an apoplastic loader, and cotton’s close relatedness to Tilia spp. hints at passive loading. Suc was the only canonical transport sugar in leaves and constituted 87% of 14C-labeled photoassimilate being actively transported. [14C]Suc uptake coupled with autoradiography indicated active [14C]Suc accumulation in minor veins, suggesting Suc loading from the apoplast; esculin, a fluorescent Suc analog, did not accumulate in minor veins. Of the nine sucrose transporter (SUT) genes identified per diploid genome, only GhSUT1-L2 showed appreciable expression in mature leaves, and silencing GhSUT1-L2 yielded phenotypes characteristic of blocked phloem transport. Furthermore, only GhSUT1-L2 cDNA stimulated esculin and [14C]Suc uptake into yeast, and only the GhSUT1-L2 promoter caused uidA (β-glucuronidase) reporter gene expression in minor vein phloem of Arabidopsis thaliana. Collectively, these results argue that apoplastic phloem loading mediated by GhSUT1-L2 is the dominant mode of phloem loading in cotton.

Severe developmental disability in children affects the life of the child and entire household. We conducted a qualitative study to understand how caregivers manage severe developmental disabilities in children in rural Africa. Families and six children (out of 15 children) who had serious permanent sequelae from a cerebral infection in Handeni, Tanzania, were contacted and invited to a workshop to recount their experience living with severe developmental disabilities. After consent, individual interviews were conducted first through recording of individual digital stories and then through individual semi-structured interviews. Pre-determined key categories were used to analyse the data. Our results showed that developmental disabilities required constant care and reduced the autonomy of the children. Schooling had not been attempted or was halted because of learning problems or inability to meet specialized school costs. Parents were under constant physical, emotional and financial stress. Their occupational earnings decreased. Some families sold their assets to survive. Others began to rely on relatives. Understanding the consequences of developmental disability helps to identify where social support should be focused and improved.

Aerococcus urinae (A. urinae) is primarily recognized as a common pathogen in the geriatric population, causing urinary tract infection (UTI), sepsis, and endocarditis, predominantly in female patients. In the paediatric population, only a few case reports exist suggesting A. urinae causes malodorous urine in otherwise healthy boys. In this study, we investigated the spectrum of clinical and laboratory presentations of A. urinae detection in children. A retrospective, single-centre, case series including all patients with the detection of A. urinae during a 7-year study period. Patients with detection of A. urinae only in non-urogenital skin swabs were excluded. A total of 40 samples from 33 patients were identified of which 20 patients were included in the final analysis. The median (IQR) age was 6.8 (2.9–9.5) years; 18 (90%) patients were boys. Four patients were diagnosed with a UTI, six had malodorous urine without UTI, three were diagnosed with balanitis and seven showed A. urinae colonization in the urine culture. Urogenital disorders were present in 12 patients. Additional pathogens were detected in 13 patients. Recurrence of detection during our study period was observed in four (20%) patients. Conclusion: Beyond malodorous urine, A. urinae detection is associated with more severe presentations including UTI in the paediatric population. Pre-existing urogenital disorders were frequent, and therefore, a nephro-urological investigation should be considered in all cases of A. urinae detection in the paediatric population. What is Known:• Aerococcus urinae (A. urinae) is known to be a common pathogen in the geriatric population, causing urinary tract infection (UTI), sepsis, and endocarditis, predominantly in female patients.• In the paediatric population, A. urinae is mainly described as a low-grade pathogen. Some case reports describe A. urinae as the cause of extraordinary malodorous urine in otherwise healthy boys. What is New:• Beyond malodorous urine, A. urinae detection is associated with more severe presentations including UTI in the paediatric population.• A. urinae was mainly detected in boys with pre-existing urogenital disorders; therefore, a nephro-urological investigation should be considered in cases of A. urinae detection in the paediatric population.

Abstract In recent years, paleoneurology became a very popular research field and hundreds of brain-endocasts were described. The interpretation of a dorsal protuberance of the brain-endocast puzzled researchers for a long time, the so-called (cartilaginous) rider. This is mainly because of technical limitations in the past and due to non-accessibility of comparative material. Using turtles as a case-study, we conducted a literature review and studied embryological data in addition to fossil and extant species’ endocasts. We assessed three hypotheses on the origin of the rider as relating to 1) the pineal gland, to 2) the blood vessel system, and to 3) skull roof elements. Based on our integrated anatomical observations, we refute the pineal gland hypothesis (1) and an exclusive blood vessel explanation (2). However, we show that, in most cases, the cartilaginous origin applies (3). The related cartilages, mainly the anterior process of the chondrocranial tectum synoticum, can persist until adulthood. Its diversity is interpreted in regard to the mechanical support for the temporal skull region, the shape of which has been shown to be in turn related to neck retraction and jaw mechanics. Finally, we highlight the value of embryological data to provide profound hypotheses for evolutionary research despite its low quantitative evaluability. We argue that it should be studied in conjunction with modern computer-aided data acquisition whenever possible.

Contains fulltext : 244005.pdf (Publisher’s version ) (Open Access) The complement system is an important defense mechanism against pathogens; however, in certain pathologies, the system also attacks human cells, such as red blood cells (RBCs). In paroxysmal nocturnal hemoglobinuria (PNH), RBCs lack certain complement regulators which sensitize them to complement-mediated lysis, while in autoimmune hemolytic anemia (AIHA), antibodies against RBCs may initiate complement-mediated hemolysis. In recent years, complement inhibition has improved treatment prospects for these patients, with eculizumab now the standard of care for PNH patients. Current complement inhibitors are however not sufficient for all patients, and they come with high costs, patient burden, and increased infection risk. This review gives an overview of the underlying pathophysiology of complement-mediated hemolysis in PNH and AIHA, the role of therapeutic complement inhibition nowadays, and the high number of complement inhibitors currently under investigation, as for almost every complement protein, an inhibitor is being developed. The focus lies with novel therapeutics that inhibit complement activity specifically in the pathway that causes pathology or those that reduce costs or patient burden through novel administration routes.

Correct transcription is crucial for life. However, DNA damage severely impedes elongating RNA polymerase II, causing transcription inhibition and transcription-replication conflicts. Cells are equipped with intricate mechanisms to counteract the severe consequence of these transcription-blocking lesions. However, the exact mechanism and factors involved remain largely unknown. Here, using a genome-wide CRISPR–Cas9 screen, we identified the elongation factor ELOF1 as an important factor in the transcription stress response following DNA damage. We show that ELOF1 has an evolutionarily conserved role in transcription-coupled nucleotide excision repair (TC-NER), where it promotes recruitment of the TC-NER factors UVSSA and TFIIH to efficiently repair transcription-blocking lesions and resume transcription. Additionally, ELOF1 modulates transcription to protect cells against transcription-mediated replication stress, thereby preserving genome stability. Thus, ELOF1 protects the transcription machinery from DNA damage via two distinct mechanisms.

International audience; The objective of this study was to investigate the effect of altering autumn pasture availability and farm system intensity on the productivity of spring-calving dairy cows during autumn. A total of 144 Holstein-Friesian and Holstein-Friesian × Jersey crossbred dairy cows were randomly assigned to 2 whole farm system (FS) intensities and 3 autumn pasture availability (PA; measured above 3.5 cm) treatments in a 2 × 3 factorial arrangement. The 2 farm systems consisted of a medium intensity (MI: 2.75 cows/ha, target postgrazing sward height of 4.0-4.5 cm) and high intensity system (HI: 3.25 cows/ha, target postgrazing sward height of 3.5-4.0 cm, + 1.8 kg of concentrate dry matter [(DM)/cow per day]. Within each farm system treatment, cows were further subdivided into 3 different PA management strategies: high PA (HPA), medium PA (MPA), and low PA (LPA). The experimental period lasted for 11 wk from September 1 to housing of all animals on November 20 (±2 d) over 3 yr (2017-2019, inclusive). To establish the different average pasture covers for each PA treatment during autumn and in particular at the end of the grazing season, grazing rotation length was extended by +13 and +7 d for HPA and MPA, respectively, beyond that required by LPA (37 d). There were no significant FS × PA interactions for any of the pasture, dry matter intake, or milk production and composition variables analyzed. There were also no differences in pregrazing sward characteristics or sward nutritive value between FS with the exception of daily herbage allowance, which was reduced for HI system (12.2 vs. 14.2 kg of DM/cow). Milk and milk solid yield were greater for HI groups (15.9 and 1.55 kg/cow per day, respectively) compared with MI (15.4 and 1.50 kg/cow per day, respectively). Mean paddock pregrazing herbage mass was significantly higher with increased PA ranging from a mean of 1,297 kg of DM/ha for LPA to 1,718 and 2,111 kg of DM/ha of available pasture for MPA and HPA, respectively. Despite large differences in pregrazing herbage mass, there was no difference in cumulative pasture production and only modest differences in grazing efficiency and sward nutritive value between PA treatments. On average, closing pasture covers were 420, 650, and 870 kg of DM/ha for LPA, MPA, and HPA, respectively, on December 1. In addition to maintaining similar grazing season lengths and achieving big differences in availability of pasture on farm into late autumn, PA treatment had no significant effect on dry matter intake, milk production, and body condition score during the study period. The results of this study indicate that greater cow performance and pasture utilization can be achieved through a greater daily concentrate allocation along with an increased stocking rate. Moreover, the potential to adapt grazing management practices to increase the average autumn pasture cover in intensive grazing systems is highlighted. In addition, a high dependence on high-quality grazed pasture during late autumn can be ensured without compromising grazing season length while also allowing additional pasture to be available for the subsequent spring.

A new long-snouted Corydoras species is described from two tributaries of the rio Manuripe and a tributary of the rio Madre de Dios, rio Madeira basin, Peru. Corydoras fulleri can be distinguished from its congeners by having the following features: (I) branch of the temporal sensory canal at sphenotic, which gives rise to the supraorbital canal, with two pores; (III) upper tooth plate of branchial arch with three series of teeth; (III) area at the corner of the mouth, ventral to the maxillary barbel, with a small fleshy flap; (IV) two moderate-sized dark brown or black blotches on caudal-fin base, one on its lateral portion and another one on its dorsal portion, blotches variably diffuse and/or fused with each other; (V) absence of a dark brown or black stripe transversally crossing the orbit; (VI) a longitudinal dark brown or black stripe on postdorsal region of flank midline, variably fused with the lateral peduncular blotch, some specimens with slender, longitudinally elongated, dark brown or black blotch on flank midline, forming a dash-like marking, stripe or dash-like blotch diffuse in some specimens; and (VII) region around dorsal-fin origin generally lacking dark brown or black blotch, or displaying diffuse blotch. This article is protected by copyright. All rights reserved.

Vitamins are essential compounds to yeasts, and notably in winemaking contexts. Vitamins are involved in numerous yeast metabolic pathways, including those of amino acids, fatty acids, and alcohols, which suggests their notable implication in fermentation courses, as well as in the development of aromatic compounds in wines. Although they are major components in the course of those microbial processes, their significance and impact have not been extensively studied in the context of winemaking and wine products, as most of the studies focusing on the subject in the past decades have relied on relatively insensitive and imprecise analytical methods. Therefore, this review provides an extensive overview of the current knowledge regarding the impacts of vitamins on grape must fermentations, wine-related yeast metabolisms, and requirements, as well as on the profile of wine sensory characteristics. We also highlight the methodologies and techniques developed over time to perform vitamin analysis in wines, and assess the importance of precisely defining the role played by vitamins in winemaking processes, to ensure finer control of the fermentation courses and product characteristics in a highly complex matrix.

Metabolism and mechanics are intrinsically intertwined. External forces, sensed through the cytoskeleton or distortion of the cell and organelles, induce metabolic changes in the cell. The resulting changes in metabolism, in turn, feed back to regulate every level of cell biology, including the mechanical properties of cells and tissues. Here we examine the links between metabolism and mechanics, highlighting signalling pathways involved in the regulation and response to cellular mechanosensing. We consider how forces and metabolism regulate one another through nanoscale molecular sensors, micrometre-scale cytoskeletal networks, organelles and dynamic biomolecular condensates. Understanding this cross-talk will create diagnostic and therapeutic opportunities for metabolic disorders such as cancer, cardiovascular pathologies and obesity.

Understanding how risk factors affect populations across their annual cycle is a major challenge for conserving migratory birds. For example, disease outbreaks may happen on the breeding grounds, the wintering grounds, or during migration and are expected to accelerate under climate change. The ability to identify the geographic origins of impacted individuals, especially outside of breeding areas, might make it possible to predict demographic trends and inform conservation decision‐making. However, such an effort is made more challenging by the degraded state of carcasses and resulting low quality of DNA available. Here, we describe a rapid and low‐cost approach for identifying the origins of birds sampled across their annual cycle that is robust even when DNA quality is poor. We illustrate the approach in the common loon (Gavia immer), an iconic migratory aquatic bird that is under increasing threat on both its breeding and wintering areas. Using 300 samples collected from across the breeding range, we develop a panel of 158 single‐nucleotide polymorphisms (SNP) loci with divergent allele frequencies across six genetic subpopulations. We use this SNP panel to identify the breeding grounds for 142 live nonbreeding individuals and carcasses. For example, genetic assignment of loons sampled during botulism outbreaks in parts of the Great Lakes provides evidence for the significant role the lakes play as migratory stopover areas for loons that breed across wide swaths of Canada, and highlights the vulnerability of a large segment of the breeding population to botulism outbreaks that are occurring in the Great Lakes with increasing frequency. Our results illustrate that the use of SNP panels to identify breeding origins of carcasses collected during the nonbreeding season can improve our understanding of the population‐specific impacts of mortality from disease and anthropogenic stressors, ultimately allowing more effective management.

The Kilombero Valley, one of East Africa’s largest seasonal wetlands, is a high-potential agricultural development corridor area in Tanzania. This seasonally flooded wetland is mainly used by smallholder farmers who cultivate during the rainy season, although there are some community-based irrigation systems that reduce hydro-climatic risks. In this study, we aim to understand how farmers’ aspirations and visions about the future are related to the current agricultural practices and human–water interaction. We specifically investigate the differences between farmers from rainfed and irrigated agriculture by using focus group discussions. Analysis of the in-depth interviews highlights how farmers’ actions both shape and respond to this highly dynamic and uncertain environment. Furthermore, we identify a close link, driven by the farmers’ level of agency, between aspirations and expected agro-economic development. The heterogeneity of farmers’ agency and hence their ability to cope with change is not only based on the socioeconomic status but also on their perception of the physical environment. We thus recommend that attention is also paid to the capacity for coping with environmental challenges that influences the level of farmers’ aspiration.

Triple negative breast cancer (TNBC) is an aggressive disease with a 5-y relative survival rate of 11% after distant metastasis. To survive the metastatic cascade, tumor cells remodel their signaling pathways by regulating energy production and upregulating survival pathways. AMP-activated protein kinase (AMPK) and Akt regulate energy homeostasis and survival, however, the individual or synergistic role of AMPK and Akt isoforms during lung colonization by TNBC cells is unknown. The purpose of this study was to establish whether targeting Akt, AMPKα or both Akt and AMPKα isoforms in circulating cancer cells can suppress TNBC lung colonization. Transient silencing of Akt1 or Akt2 dramatically decreased metastatic colonization of lungs by inducing apoptosis or inhibiting invasion, respectively. Importantly, transient pharmacologic inhibition of Akt activity with MK-2206 or AZD5363 inhibitors did not prevent colonization of lung tissue by TNBC cells. Knockdown of AMPKα1, AMPKα2, or AMPKα1/2 also had no effect on metastatic colonization of lungs. Taken together, these findings demonstrate that transient decrease in AMPK isoforms expression alone or in combination with Akt1 in circulating tumor cells does not synergistically reduce TNBC metastatic lung colonization. Our results also provide evidence that Akt1 and Akt2 expression serve as a bottleneck that can challenge colonization of lungs by TNBC cells.

We review the case for improving photosynthesis to increase yields in C4 crops, and highlight potential strategies to alleviate bottlenecks limiting C4 photosynthetic performance under optimal and suboptimal conditions., Although improving photosynthetic efficiency is widely recognized as an underutilized strategy to increase crop yields, research in this area is strongly biased towards species with C3 photosynthesis relative to C4 species. Here, we outline potential strategies for improving C4 photosynthesis to increase yields in crops by reviewing the major bottlenecks limiting the C4 NADP-malic enzyme pathway under optimal and suboptimal conditions. Recent experimental results demonstrate that steady-state C4 photosynthesis under non-stressed conditions can be enhanced by increasing Rubisco content or electron transport capacity, both of which may also stimulate CO2 assimilation at supraoptimal temperatures. Several additional putative bottlenecks for photosynthetic performance under drought, heat, or chilling stress or during photosynthetic induction await further experimental verification. Based on source–sink interactions in maize, sugarcane, and sorghum, alleviating these photosynthetic bottlenecks during establishment and growth of the harvestable parts are likely to improve yield. The expected benefits are also shown to be augmented by the increasing trend in planting density, which increases the impact of photosynthetic source limitation on crop yields.

Pleurodires are less diverse than cryptodires, together forming the two major lineages of crown turtles. Their fossil record, however, is rich. A particularly large number of fossil pleurodires, many belonging to the Podocnemidoidae, has been recovered from the Upper Cretaceous Bauru Group outcrops of south‐central Brazil. Herein we describe an additional pleurodire from this region, Amabilis uchoensis gen. et sp. nov., based on a partially preserved skull. A. uchoensis is recognized as belonging to the Podocnemidoidae by the small entrance to the antrum postoticum and completely developed cavum pterygoidei, being unique among other non‐podocnemidid podocnemidoids for its medially open fenestra postotica and absent basioccipital–opisthotic contact. Our cladistic analysis places A. uchoensis as a sister taxon to Hamadachelys + other podocnemidoids. We further explore the neuroanatomy of side‐necked turtles with the aid of micro‐computed tomography of specimens of the main pleurodiran lineages. Our data shed light on the different carotid circulation patterns in pleurodires, and we propose new phylogenetic characters to describe the neuroanatomical variation of the group. Optimization of these characters shows two independent acquisitions of a foramen for the palatal branch of the carotid in chelids and podocnemidoids, and a unique loss of the vidian nerve canal in chelids, in turtles in general., Fundação de Amparo à Pesquisa do Estado de São Paulo, Natural Environment Research Council http://dx.doi.org/10.13039/501100000270

This paper describes the diagnostic criteria for “Vestibular Migraine of Childhood”, “probable Vestibular Migraine of Childhood” and “Recurrent Vertigo of Childhood” as put forth by the Committee for the Classification of Vestibular Disorders of the Bárány Society (ICVD) and the Migraine Classification subgroup of the International Headache Society. Migraine plays an important role in some subgroups of children with recurrent vertigo. In this classification paper a spectrum of three disorders is described in which the migraine component varies from definite to possibly absent. These three disorders are: Vestibular Migraine of Childhood, probable Vestibular Migraine of Childhood and Recurrent Vertigo of Childhood. The criteria for Vestibular Migraine of Childhood (VMC) include (A) at least five episodes with vestibular symptoms of moderate or severe intensity, lasting between five minutes and 72 hours, (B) a current or past history of migraine with or without aura, and (C) at least half of episodes are associated with at least one migraine feature. Probable Vestibular Migraine of Childhood (probable VMC) is considered when at least three episodes with vestibular symptoms of moderate or severe intensity, lasting between five minutes and 72 hours, are accompanied by at least criterion B or C from the VMC criteria. Recurrent Vertigo of Childhood (RVC) is diagnosed in case of at least three episodes with vestibular symptoms of moderate or severe intensity, lasting between 1 minute and 72 hours, and none of the criteria B and C for VMC are applicable. For all disorders, the age of the individual needs to be below 18 years old. It is recommended that future research should particularly focus on RVC, in order to investigate and identify possible subtypes and its links or its absence thereof with migraine.

Understanding the effects of climate on the vital rates (e.g., survival, development, reproduction) and dynamics of natural populations is a long-standing quest in ecology, with ever-increasing relevance in the face of climate change. However, linking climate drivers to demographic processes requires identifying the appropriate time windows during which climate influences vital rates. Researchers often do not have access to the long-term data required to test a large number of windows, and are thus forced to make a priori choices. In this study, we first synthesize the literature to assess current a priori choices employed in studies performed on 104 plant species that link climate drivers with demographic responses. Second, we use a sliding-window approach to investigate which combination of climate drivers and temporal window have the best predictive ability for vital rates of four perennial plant species that each have over a decade of demographic data (Helianthella quinquenervis, Frasera speciosa, Cylindriopuntia imbricata, and Cryptantha flava). Our literature review shows that most studies consider time windows in only the year preceding the measurement of the vital rate(s) of interest, and focus on annual or growing season temporal scales. In contrast, our sliding-window analysis shows that in only four out of 13 vital rates the selected climate drivers have time windows that align with, or are similar to, the growing season. For many vital rates, the best window lagged more than 1 year and up to 4 years before the measurement of the vital rate. Our results demonstrate that for the vital rates of these four species, climate drivers that are lagged or outside of the growing season are the norm. Our study suggests that considering climatic predictors that fall outside of the most recent growing season will improve our understanding of how climate affects population dynamics.

Dominant species in intercropping experience less resource competition compared with its monoculture. This reduced competition for resources may allow cultivating the dominant species at an increased density in intercropping to obtain greater yield. However, experimental results are inconclusive when the optimal within row density in the sole crop is not well established. Here, we conducted a two‐year experiment to test the hypothesis that optimal within row plant density of dominant species in intercropping would be higher in the intercrop than in the sole crop. We tested three maize densities (3, 4.5, and 6 plants m−1) in both sole maize and two replacement designed intercrops. The row configurations of two intercrops are two rows maize intercropped with four rows peanut (M2P4) and four rows maize intercropped with four rows peanut (M4P4). Peanut was grown at the same plant density of 12 plants m−1 row in both sole crop and intercrops. The results indicated that increasing maize density from the optimal density in monoculture is not worthy of promotion to improve yield in intercropping, which denied our hypothesis. The land equivalent ratios (LER) in the dry year (2017) were higher than the wet year (2016). Maize yields per unit area of the whole intercropping system were highest with densities of 4.5 and 6 plants m−1 row, with no significant difference between these two densities. Maximum maize yields in sole cropping were obtained with maize densities of 6 plants m−1 row. Intercropping provided higher yields at low and intermediate sole crop maize densities, but not at high sole crop maize density. Average land equivalent ratios at 3, 4.5, and 6 plants m−1 of maize were 1.09, 1.04, and 0.95 in 2016, and 1.07, 1.10, and 1.02 in 2017. Our results suggest that intercropping performs better at conditions with less resources than adequate resources.

Methylomirabilis bacteria perform anaerobic methane oxidation coupled to nitrite reduction via an intra-aerobic pathway, producing carbon dioxide and dinitrogen gas. These diderm bacteria possess an unusual polygonal cell shape with sharp ridges that run along the cell body. Previously, a putative surface protein layer (S-layer) was observed as the outermost cell layer of these bacteria. We hypothesized that this S-layer is the determining factor for their polygonal cell shape. Therefore, we enriched the S-layer from M. lanthanidiphila cells and through LC-MS/MS identified a 31 kDa candidate S-layer protein, mela_00855, which had no homology to any other known protein. Antibodies were generated against a synthesized peptide derived from the mela_00855 protein sequence and used in immunogold localization to verify its identity and location. Both on thin sections of M. lanthanidiphila cells and in negative-stained enriched S-layer patches, the immunogold localization identified mela_00855 as the S-layer protein. Using electron cryo-tomography and sub-tomogram averaging of S-layer patches, we observed that the S-layer has a hexagonal symmetry. Cryo-tomography of whole cells showed that the S-layer and the outer membrane, but not the peptidoglycan layer and the cytoplasmic membrane, exhibited the polygonal shape. Moreover, the S-layer consisted of multiple rigid sheets that partially overlapped, most likely giving rise to the unique polygonal cell shape. These characteristics make the S-layer of M. lanthanidiphila a distinctive and intriguing case to study.

Objective Adult polyglucosan body disease (APBD) is an adult‐onset neurological variant of glycogen storage disease type IV. APBD is caused by recessive mutations in the glycogen branching enzyme gene, and the consequent accumulation of poorly branched glycogen aggregates called polyglucosan bodies in the nervous system. There are presently no treatments for APBD. Here, we test whether downregulation of glycogen synthesis is therapeutic in a mouse model of the disease. Methods We characterized the effects of knocking out two pro‐glycogenic proteins in an APBD mouse model. APBD mice were crossed with mice deficient in glycogen synthase (GYS1), or mice deficient in protein phosphatase 1 regulatory subunit 3C (PPP1R3C), a protein involved in the activation of GYS1. Phenotypic and histological parameters were analyzed and glycogen was quantified. Results APBD mice deficient in GYS1 or PPP1R3C demonstrated improvements in life span, morphology, and behavioral assays of neuromuscular function. Histological analysis revealed a reduction in polyglucosan body accumulation and of astro‐ and micro‐gliosis in the brains of GYS1‐ and PPP1R3C‐deficient APBD mice. Brain glycogen quantification confirmed the reduction in abnormal glycogen accumulation. Analysis of skeletal muscle, heart, and liver found that GYS1 deficiency reduced polyglucosan body accumulation in all three tissues and PPP1R3C knockout reduced skeletal muscle polyglucosan bodies. Interpretation GYS1 and PPP1R3C are effective therapeutic targets in the APBD mouse model. These findings represent a critical step toward the development of a treatment for APBD and potentially other glycogen storage disease type IV patients.

Researchers were asked to contribute new results addressing questions about the exposure and effects of mercury (Hg) in North American songbirds, a rapidly declining group of species that is the subject of enduring interest for millions of birdwatchers, the general public and conservation scientists. Important questions to be answered include: Is Hg causing or exacerbating songbird population declines? Which North American songbirds are at most risk and in which landscapes? Are there aspects of songbird natural history that pre-dispose them to risks of Hg exposure and effects, in particular, their migratory behavior? In all, 61 authors contributed 15 studies addressing aspects of these questions. Articles in this special issue address an array of topics including: (1) three studies on health effects in the laboratory using a domesticated songbird model species, the zebra finch; (2) three studies on changes in songbird exposure to Hg over time spans from less than a decade to more than a century; (3) five studies on landscape characteristics or management practices that cause the oft-noted spatial variation in Hg accumulation by resident songbirds, from the subarctic tundra to high-elevation tropical forests; (4) three papers examining the recently recognized role of migration behavior in predicting risk to songbirds from Hg; and (5) one paper on the potential pitfalls of using feather Hg concentration as a bioindicator for Hg exposure. In summary, although there are many questions still to be answered, it is clear that the effects of Hg are persistent long after exposure, Hg exposure of North American songbirds is not improving, predicting exposure requires a detailed understanding of ecosystem processes beyond simply the amount of Hg present at a site, migration behavior predisposes songbirds to risk of Hg exposure and effects, and carefully selecting appropriate bioindicator sites, species, and tissues is critical to any monitoring efforts.

Wnt signaling dysregulation promotes tumorigenesis in colorectal cancer (CRC). We investigated the role of PTPRF, a receptor-type tyrosine phosphatase, in regulating Wnt signaling in CRC. Knockdown of PTPRF decreased cell proliferation in patient-derived primary colon cancer cells and established CRC cell lines. In addition, the rate of proliferation as well as colony formation ability were significantly decreased cells in tumor organoids grown in 3D, whereas the number of differentiated tumor organoids were markedly increased. Consistently, knockdown of PTPRF resulted in a decrease in the expression of genes associated cancer stem cells downstream of Wnt/β-catenin signaling. Treating PTPRF knockdown cells with GSK3 inhibitor rescued the expression of Wnt target genes suggesting that PTPRF functions upstream of the β-catenin destruction complex. PTPRF was found to interact with LRP6 and silencing PTPRF largely decreased the activation of LRP6. Interestingly, this PTPRF-mediated activation of Wnt signaling was blocked in cells treated with clathrin endocytosis inhibitor. Furthermore, knockdown of PTPRF inhibited xenograft tumor growth in vivo and decreased the expression of Wnt target genes. Taken together, our studies identify a novel role of PTPRF as an oncogenic protein phosphatase in supporting the activation of Wnt signaling in CRC.

Phenylketonuria (PKU), caused by variants in the phenylalanine hydroxylase (PAH) gene, is the most common autosomal-recessive Mendelian phenotype of amino acid metabolism. We estimated that globally 0.45 million individuals have PKU, with global prevalence 1:23,930 live births (range 1:4,500 [Italy]–1:125,000 [Japan]). Comparing genotypes and metabolic phenotypes from 16,092 affected subjects revealed differences in disease severity in 51 countries from 17 world regions, with the global phenotype distribution of 62% classic PKU, 22% mild PKU, and 16% mild hyperphenylalaninemia. A gradient in genotype and phenotype distribution exists across Europe, from classic PKU in the east to mild PKU in the southwest and mild hyperphenylalaninemia in the south. The c.1241A>G (p.Tyr414Cys)-associated genotype can be traced from Northern to Western Europe, from Sweden via Norway, to Denmark, to the Netherlands. The frequency of classic PKU increases from Europe (56%) via Middle East (71%) to Australia (80%). Of 758 PAH variants, c.1222C>T (p.Arg408Trp) (22.2%), c.1066−11G>A (IVS10−11G>A) (6.4%), and c.782G>A (p.Arg261Gln) (5.5%) were most common and responsible for two prevalent genotypes: p.[Arg408Trp];[Arg408Trp] (11.4%) and c.[1066−11G>A];[1066−11G>A] (2.6%). Most genotypes (73%) were compound heterozygous, 27% were homozygous, and 55% of 3,659 different genotypes occurred in only a single individual. PAH variants were scored using an allelic phenotype value and correlated with pre-treatment blood phenylalanine concentrations (n = 6,115) and tetrahydrobiopterin loading test results (n = 4,381), enabling prediction of both a genotype-based phenotype (88%) and tetrahydrobiopterin responsiveness (83%). This study shows that large genotype databases enable accurate phenotype prediction, allowing appropriate targeting of therapies to optimize clinical outcome. Fil: Hillert, Alicia. No especifíca; Fil: Anikster, Yair. No especifíca; Fil: Belanger Quintana, Amaya. No especifíca; Fil: Burlina, Alberto. No especifíca; Fil: Burton, Barbara K.. No especifíca; Fil: Carducci, Carla. No especifíca; Fil: Chiesa, Ana Elena. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Investigaciones Endocrinológicas "Dr. César Bergada". Gobierno de la Ciudad de Buenos Aires. Centro de Investigaciones Endocrinológicas "Dr. César Bergada". Fundación de Endocrinología Infantil. Centro de Investigaciones Endocrinológicas "Dr. César Bergada"; Argentina Fil: Christodoulou, John. No especifíca; Fil: Dordevic, Maja. No especifíca; Fil: Desviat, Lourdes R.. No especifíca; Fil: Eliyahu, Aviva. No especifíca; Fil: Evers, Roeland A.F.. No especifíca; Fil: Fajkusova, Lena. No especifíca; Fil: Feillet, Francois. No especifíca; Fil: Bonfim Freitas, Pedro E.. No especifíca; Fil: Gizewska, María. No especifíca; Fil: Gundorova, Polina. No especifíca; Fil: Karall, Daniela. No especifíca; Fil: Kneller, Katya. No especifíca; Fil: Kutsev, Sergey I.. No especifíca; Fil: Leuzzi, Vincenzo. No especifíca; Fil: Levy, Harvey L.. No especifíca; Fil: Lichter Koneck, Uta. No especifíca; Fil: Muntau, Ania C.. No especifíca; Fil: Namour, Fares. No especifíca; Fil: Oltarzewsk, Mariusz. No especifíca; Fil: Paras, Andrea. No especifíca; Fil: Perez, Belén. No especifíca; Fil: Polak, Emil. No especifíca; Fil: Polyakov, Alexander V.. No especifíca; Fil: Porta, Francesco. No especifíca; Fil: Rohrbach, Marianne. No especifíca; Fil: Scholl Bürgi, Sabine. No especifíca; Fil: Spécola, Norma. No especifíca; Fil: Stojiljkovic, Maja. No especifíca; Fil: Shen, Nan. No especifíca; Fil: Santana da Silva, Luiz C.. No especifíca; Fil: Skouma, Anastasia. No especifíca; Fil: van Spronsen, Francjan. No especifíca; Fil: Stoppioni, Vera. No especifíca; Fil: Thöny, Beat. No especifíca; Fil: Trefz, Friedrich K.. No especifíca; Fil: Vockley, Jerry. No especifíca; Fil: Yu, Youngguo. No especifíca; Fil: Zschocke, Johannes. No especifíca; Fil: Hoffmann, Georg F.. No especifíca; Fil: Garbade, Sven F.. No especifíca; Fil: Blau, Nenad. No especifíca

Background Respiratory syncytial virus (RSV) is a global cause of severe respiratory morbidity and mortality in infants. While preventive and therapeutic interventions are being developed, including antivirals, vaccines and monoclonal antibodies, little is known about the global molecular epidemiology of RSV. INFORM is a prospective, multicenter, global clinical study performed by ReSViNET to investigate the worldwide molecular diversity of RSV isolates collected from children less than 5 years of age. Methods The INFORM study is performed in 17 countries spanning all inhabited continents and will provide insight into the molecular epidemiology of circulating RSV strains worldwide. Sequencing of > 4000 RSV-positive respiratory samples is planned to detect temporal and geographical molecular patterns on a molecular level over five consecutive years. Additionally, RSV will be cultured from a subset of samples to study the functional implications of specific mutations in the viral genome including viral fitness and susceptibility to different monoclonal antibodies. Discussion The sequencing and functional results will be used to investigate susceptibility and resistance to novel RSV preventive or therapeutic interventions. Finally, a repository of globally collected RSV strains and a database of RSV sequences will be created.

Cancer cells express high levels of programmed death ligand 1 (PD-L1), a ligand of the programmed cell death protein 1 (PD-1) receptor on T cells, allowing tumors to suppress T cell activity. Clinical trials utilizing antibodies that disrupt the PD-1/PD-L1 checkpoint have yielded remarkable results, with anti-PD-1 immunotherapy approved as a first-line therapy for patients with lung cancer. We used CRISPR-based screening to identify regulators of PD-L1 in human lung cancer cells, revealing potent induction of PD-L1 upon disruption of heme biosynthesis. Impairment of heme production activates the integrated stress response, allowing bypass of inhibitory upstream open reading frames in the PD-L1 5′ untranslated region, resulting in enhanced PD-L1 translation and suppression of anti-tumor immunity. We demonstrate that integrated stress-response-dependent PD-L1 translation requires the translation initiation factor eIF5B. eIF5B overexpression, which is frequent in lung adenocarcinomas and associated with poor prognosis, is sufficient to induce PD-L1. These findings illuminate mechanisms of immune checkpoint activation and identify targets for therapeutic intervention. O’Donnell and colleagues report that activation of the integrated stress response in non-small cell lung cancer cells by impairing heme production leads to enhanced PD-L1 translation in an eIF5B-dependent manner.

ObjectiveTo assess whether women with atrial fibrillation (AF) have a higher risk of adverse events than men during long-term follow-up since controversial data have been published.MethodsIn the context of two very similar observational multicentre cohort studies, we prospectively followed 3894 patients (28% women) with previously documented AF for a median of 4.02 (3.00–5.83) years. The primary outcome was a composite of ischaemic stroke, myocardial infarction and cardiovascular death. Secondary outcomes included the individual components of the composite outcome, hospitalisation for heart failure, major and clinically relevant non-major bleeding, stroke or systemic embolism and non-cardiovascular death.ResultsMean age was 73.1 years in women vs 70.8 years in men. The incidence of the primary endpoint in women versus men was 2.46 vs 3.24 per 100 patient-years, respectively (adjusted HR (aHR) 0.74, 95% CI 0.58 to 0.94; p=0.01). Women died less frequently from cardiovascular (aHR 0.57, 95% CI 0.41 to 0.78; pConclusionIn this large study of patients with established AF, women had a lower risk of death than men, but there were no sex-specific differences in other adverse outcomes.

Summary Monocytes continuously adapt their shapes for proper circulation and elicitation of effective immune responses. Although these functions depend on the cell mechanical properties, the mechanical behavior of monocytes is still poorly understood and accurate physiologically relevant data on basic mechanical properties are lacking almost entirely. By combining several complementary single-cell force spectroscopy techniques, we report that the mechanical properties of human monocyte are strain-rate dependent, and that chemokines can induce alterations in viscoelastic behavior. In addition, our findings indicate that human monocytes are heterogeneous mechanically and this heterogeneity is regulated by chemokine CCL2. The technology presented here can be readily used to reveal mechanical complexity of the blood cell population in disease conditions, where viscoelastic properties may serve as physical biomarkers for disease progression and response to therapy., Graphical abstract, Highlights • Mechanical properties of monocytes are affected by temperature changes • Mechanical properties of monocytes are strain-rate dependent • CCL2 affects both the viscous and elastic properties of monocytes • CCL2 potentially modulates monocytes mechanically to transit to a primed state, Immunology; Cell biology; Biomechanics

Background As a step towards clinical use of AAV-mediated gene therapy, brains of large animals are used to settle delivery parameters as most brain connections, and relative sizes in large animals and primates, are reasonably common. Prior to application in the clinic, approaches that have shown to be successful in rodent models are tested in larger animal species, such as dogs, non-human primates, and in this case, minipigs. New method We evaluated alternate delivery routes to target the basal ganglia by injections into the more superficial corona radiata, and, deeper into the brain, the thalamus. Anatomically known connections can be used to predict the expression of the transgene following infusion of AAV5. For optimal control over delivery of the vector with regards to anatomical location in the brain and spread in the tissue, we have used magnetic resonance image-guided convection-enhanced diffusion delivery. Results While the transduction of the cortex was observed, only partial transduction of the basal ganglia was achieved via the corona radiata. Thalamic administration, on the other hand, resulted in widespread transduction from the midbrain to the frontal cortex Comparison with existing methods Compared to other methods, such as delivery directly to the striatum, thalamic injection may provide an alternative when for instance, injection into the basal ganglia directly is not feasible. Conclusions The study results suggest that thalamic administration of AAV5 has significant potential for indications where the transduction of specific areas of the brain is required.

A search for production of the superheavy elements with atomic numbers 119 and 120 was performed in the 50Ti+249Bk and 50Ti+249Cf fusion-evaporation reactions, respectively, at the gas-filled recoil separator TASCA at GSI Darmstadt, Germany. Over four months of irradiation, the 249Bk target partially decayed into 249Cf, which allowed for a simultaneous search for both elements. Neither was detected at cross-section sensitivity levels of 65 and 200 fb for the 50Ti+249Bk and 50Ti+249Cf reactions, respectively, at a midtarget beam energy of Elab=281.5 MeV. The nonobservation of elements 119 and 120 is discussed within the concept of fusion-evaporation reactions including various theoretical predictions on the fission-barrier heights of superheavy nuclei in the region of the island of stability. peerReviewed

The A-genome diploid wheats represent the earliest domesticated and cultivated wheat species in the Fertile Crescent and the donor of the wheat A sub-genome. The A-genome species encompass the cultivated einkorn (Triticum. monococcum L. subsp. monococcum), wild einkorn (T. monococcum L. subsp. aegilopoides (Link) Thell.) and T. urartu. We evaluated the collection of 930 accessions in the Wheat Genetics Resource Center (WGRC), using genotyping-by-sequencing (GBS) and identified 13,089 curated SNPs. Genomic analysis detected misclassified and duplicated accessions with most duplicates originated from the same or a nearby locations. About 56% (n = 520) of the WGRC A-genome species collections were duplicates supporting the need for genomic characterization for effective curation and maintenance of these collections. Population structure analysis confirmed the morphology-based classifications of the accessions and reflected the species geographic distributions. We also showed that the T. urartu as the closest A-genome diploid to wheat through phylogenetic analysis. Population analysis within the wild einkorn group showed three genetically distinct clusters, which corresponded with wild einkorn races α, β, and γ described previously. The T. monococcum genome-wide FST scan identified candidate genomic regions harboring domestication selection signature (Btr1) on the short arm of chromosome 3Am at ~ 70 Mb. We established A-genome core set (79 accessions) based on allelic diversity, geographical distribution, and available phenotypic data. The individual species core set maintained at least 80% of allelic variants in the A-genome collection and constitute a valuable genetic resource to improve wheat and domesticated einkorn in breeding programs.One-sentence summaryGenotyping of gene bank collections of diploid A-genome relatives of wheat uncovered relatively higher genetic diversity and unique evolutionary relationships which gives insight to the effective use of these germplasm for wheat improvement.

A primitive neuronal component is a feature of some glioblastomas but defining molecular alterations of this histologic variant remains uncertain. We performed next-generation sequencing of 1500 tumor related genes on tissue from 9 patients with glioblastoma with a primitive component (G/PN) and analyzed 27 similar cases from the Cancer Genome Atlas (TCGA) dataset. Alterations in the RB pathway were identified in all of our patients’ tumors and 81% of TCGA tumors with the retinoblastoma tumor suppressor gene (RB1) commonly affected. Although RB1 mutations were observed in some conventional glioblastomas, the allelic fractions of these mutations were significantly higher in tumors with a primitive neuronal component in both our and TCGA cohorts (median, 72% vs 25%, p

Intercropping is both a well-established and yet novel agricultural practice, depending on one’s perspective. Such perspectives are principally governed by geographic location and whether monocultural practices predominate. Given the negative environmental effects of monoculture agriculture (loss of biodiversity, reliance on non-renewable inputs, soil degradation, etc.), there has been a renewed interest in cropping systems that can reduce the impact of modern agriculture while maintaining (or even increasing) yields. Intercropping is one of the most promising practices in this regard, yet faces a multitude of challenges if it is to compete with and ultimately replace the prevailing monocultural norm. These challenges include the necessity for more complex agricultural designs in space and time, bespoke machinery, and adapted crop cultivars. Plant breeding for monocultures has focused on maximizing yield in single-species stands, leading to highly productive yet specialized genotypes. However, indications suggest that these genotypes are not the best adapted to intercropping systems. Re-designing breeding programs to accommodate inter-specific interactions and compatibilities, with potentially multiple different intercropping partners, is certainly challenging, but recent technological advances offer novel solutions. We identify a number of such technology-driven directions, either ideotype-driven (i.e., “trait-based” breeding) or quantitative genetics-driven (i.e., “product-based” breeding). For ideotype breeding, plant growth modeling can help predict plant traits that affect both inter- and intraspecific interactions and their influence on crop performance. Quantitative breeding approaches, on the other hand, estimate breeding values of component crops without necessarily understanding the underlying mechanisms. We argue that a combined approach, for example, integrating plant growth modeling with genomic-assisted selection and indirect genetic effects, may offer the best chance to bridge the gap between current monoculture breeding programs and the more integrated and diverse breeding programs of the future.

Seabirds are amongst the most mobile of all animal species and spend large amounts of their lives at sea. They cross vast areas of ocean that appear superficially featureless, and our understanding of the mechanisms that they use for navigation remains incomplete, especially in terms of available cues. In particular, several large-scale navigational tasks, such as homing across thousands of kilometers to breeding sites, are not fully explained by visual, olfactory or magnetic stimuli. Low-frequency inaudible sound, i.e., infrasound, is ubiquitous in the marine environment. The spatio-temporal consistency of some components of the infrasonic wavefield, and the sensitivity of certain bird species to infrasonic stimuli, suggests that infrasound may provide additional cues for seabirds to navigate, but this remains untested. Here, we propose a framework to explore the importance of infrasound for navigation. We present key concepts regarding the physics of infrasound and review the physiological mechanisms through which infrasound may be detected and used. Next, we propose three hypotheses detailing how seabirds could use information provided by different infrasound sources for navigation as an acoustic beacon, landmark, or gradient. Finally, we reflect on strengths and limitations of our proposed hypotheses, and discuss several directions for future work. In particular, we suggest that hypotheses may be best tested by combining conceptual models of navigation with empirical data on seabird movements and in-situ infrasound measurements.

In hard‐winter wheat (Triticum aestivum L.) breeding, the evaluation of end‐use quality is expensive and time‐consuming, being relegated to the final stages of the breeding program after selection for many traits including disease resistance, agronomic performance, and grain yield. In this study, our objectives were to identify genetic variants underlying baking quality traits through genome‐wide association study (GWAS) and develop improved genomic selection (GS) models for the quality traits in hard‐winter wheat. Advanced breeding lines (n = 462) from 2015–2017 were genotyped using genotyping‐by‐sequencing (GBS) and evaluated for baking quality. Significant associations were detected for mixograph mixing time and bake mixing time, most of which were within or in tight linkage to glutenin and gliadin loci and could be suitable for marker‐assisted breeding. Candidate genes for newly associated loci are phosphate‐dependent decarboxylase and lipid transfer protein genes, which are believed to affect nitrogen metabolism and dough development, respectively. The use of GS can both shorten the breeding cycle time and significantly increase the number of lines that could be selected for quality traits, thus we evaluated various GS models for end‐use quality traits. As a baseline, univariate GS models had 0.25–0.55 prediction accuracy in cross‐validation and from 0 to 0.41 in forward prediction. By including secondary traits as additional predictor variables (univariate GS with covariates) or correlated response variables (multivariate GS), the prediction accuracies were increased relative to the univariate model using only genomic information. The improved genomic prediction models have great potential to further accelerate wheat breeding for end‐use quality.

The development of next generation sequencing (NGS) enabled a shift from array-based genotyping to high-throughput genotyping by directly sequencing genomic libraries. Even though whole genome sequencing was initially too costly for routine analysis in large populations, such as those utilized for breeding or genetic studies, continued advancements in genome sequencing and bioinformatics have provided the opportunity to utilize whole-genome information. As new sequencing platforms can routinely provide high-quality sequencing data for sufficient genome coverage, a limitation comes in the time and high cost of library construction when multiplexing a large number of samples. Here we describe a high-throughput whole-genome skim-sequencing (skim-seq) approach that can be utilized for a broad range of genotyping and genomic characterization. Using optimized low-volume Illumina Nextera chemistry, we developed a skim-seq method and combined up to 960 samples in one multiplex library using dual index barcoding. With the dual-index barcoding, the number of samples for multiplexing can be adjusted depending on amount of data required and extended to 3,072 samples or more. Panels of double haploid wheat lines (Triticum aestivum, CDC Stanley x CDC Landmark), wheat-barley (T. aestivum x Hordeum vulgare) and wheat-wheatgrass (Triticum durum x Thinopyrum intermedium) introgression lines as well as known monosomic wheat stocks were genotyped using the skim-seq approach. Bioinformatics pipelines were developed for various applications where sequencing coverage ranged from 1x down to 0.01x per sample. Using reference genomes, we detected chromosome dosage, identified aneuploidy, and karyotyped introgression lines from the low coverage skim-seq data. Leveraging the recent advancements in genome sequencing, skim-seq provides an effective and low-cost tool for routine genotyping and genetic analysis, which can track and identify introgressions and genomic regions of interest in genetics research and applied breeding programs.

SUMMARYCohesin folds chromosomes via DNA loop extrusion. Cohesin-mediated chromosome loops regulate transcription by shaping long-range enhancer-promoter interactions, among other mechanisms. Mutations of cohesin subunits and regulators cause human developmental diseases termed cohesinopathy. Vertebrate cohesin consists of SMC1, SMC3, RAD21, and either STAG1 or STAG2. To probe the physiological functions of cohesin, we created conditional knockout (cKO) mice with Stag2 deleted in the nervous system. Stag2 cKO mice exhibit growth retardation, neurological defects, and premature death, in part due to insufficient myelination of nerve fibers. Stag2 cKO oligodendrocytes exhibit delayed maturation and downregulation of myelination-related genes. Stag2 loss reduces promoter-anchored loops at downregulated genes in oligodendrocytes. Thus, STAG2-cohesin generates promoter-anchored loops at myelination-promoting genes to facilitate their transcription. Our study implicates defective myelination as a contributing factor to cohesinopathy and establishes oligodendrocytes as a relevant cell type to explore the mechanisms by which cohesin regulates transcription.

Blockade of the CD47-SIRPα axis improves lymphoma cell killing by myeloid effector cells, which is an important effector mechanism for CD20 antibodies in vivo. The approved CD20 antibodies rituximab, ofatumumab, and obinutuzumab are of human immunoglobulin G1 (IgG1) isotype. We investigated the impact of the variable regions of these 3 CD20 antibodies when expressed as human IgA2 isotype variants. All 3 IgA2 antibodies mediated antibody-dependent cellular phagocytosis (ADCP) by macrophages and antibody-dependent cellular cytotoxicity (ADCC) by polymorphonuclear cells. Both effector mechanisms were significantly enhanced in the presence of a CD47-blocking antibody or by glutaminyl cyclase inhibition to interfere with CD47-SIRPα interactions. Interestingly, an IgA2 variant of obinutuzumab (OBI-IgA2) was consistently more potent than an IgA2 variant of rituximab (RTX-IgA2) or an IgA2 variant of ofatumumab (OFA-IgA2) in triggering ADCC. Furthermore, we observed more effective direct tumor cell killing by OBI-IgA2 compared with RTX-IgA2 and OFA-IgA2, which was caspase independent and required a functional cytoskeleton. IgA2 variants of all 3 antibodies triggered complement-dependent cytotoxicity, with OBI-IgA2 being less effective than RTX-IgA2 and OFA-IgA2. When we investigated the therapeutic efficacy of the CD20 IgA2 antibodies in different in vivo models, OBI-IgA2 was therapeutically more effective than RTX-IgA2 or OFA-IgA2. In vivo efficacy required the presence of a functional IgA receptor on effector cells and was independent of complement activation or direct lymphoma cell killing. These data characterize the functional activities of human IgA2 antibodies against CD20, which were affected by the selection of the respective variable regions. OBI-IgA2 proved particularly effective in vitro and in vivo, which may be relevant in the context of CD47-SIRPα blockade.

BackgroundThe addition of monoclonal antibody therapy against GD2 to the treatment of high-risk neuroblastoma led to improved responses in patients. Nevertheless, administration of GD2 antibodies against neuroblastoma is associated with therapy-limiting neuropathic pain. This severe pain is evoked at least partially through complement activation on GD2-expressing sensory neurons.MethodsTo reduce pain while maintaining antitumor activity, we have reformatted the approved GD2 antibody ch14.18 into the IgA1 isotype. This novel reformatted IgA is unable to activate the complement system but efficiently activates leukocytes through the FcαRI (CD89).ResultsIgA GD2 did not activate the complement system in vitro nor induced pain in mice. Importantly, neutrophil-mediated killing of neuroblastoma cells is enhanced with IgA in comparison to IgG, resulting in efficient tumoricidal capacity of the antibody in vitro and in vivo.ConclusionsOur results indicate that employing IgA GD2 as a novel isotype has two major benefits: it halts antibody-induced excruciating pain and improves neutrophil-mediated lysis of neuroblastoma. Thus, we postulate that patients with high-risk neuroblastoma would strongly benefit from IgA GD2 therapy.

Many migratory songbirds are at high risk of methylmercury (MeHg) exposure due to their trophic position and foraging in and around wetland habitats. Methylmercury has the potential to alter migratory behaviors and physiology via neurological impairment or reduced flight performance and can be remobilized from songbird muscle tissue during migration, increasing the risk of acute MeHg exposure. To document MeHg exposure and its relationship with physical condition in migratory songbirds, we sampled passerine blood and feathers at a migration stopover site on Key Biscayne, FL during fall and spring from 2009 to 2012. We found evidence that spring blood total mercury (THg) concentrations decreased throughout the day and that fall feather THg concentrations changed over the migratory season. Total mercury exposure was marginally correlated with migratory fat stores and related to changes in pectoral muscle thickness by time of day. These patterns suggest that environmentally relevant levels of THg are related to, and may be influencing, the physical condition of free-living migrating songbirds. Further research and monitoring during the migratory period will be important to elucidate exposure risk across multiple species and assess the potential for effects during this complex period of the annual cycle.

Freshwater fish in several regions of New York State (NYS) are known to contain concentrations of mercury (Hg) associated with negative health effects in wildlife and humans. We collected blood and breast feathers from bald eagle (Haliaeetus leucocephalus) nestlings throughout NYS, with an emphasis on the Catskill region to determine their exposure to Hg. We assessed whether habitat type (lake or river), region (Delaware–Catskill region vs. rest of NY) or sample site elevation influenced Hg concentrations in bald eagle breast feathers using ANCOVA. The model was significant and accounted for 41% of the variability in log10 breast feather Hg concentrations. Mercury concentrations in nestling breast feathers were significantly greater in the Delaware–Catskill Region (geometric mean: 14.5 µg/g dw) than in the rest of NY (7.4 µg/g, dw), and greater at nests located at higher elevations. Habitat type (river vs. lake) did not have a significant influence on breast feather Hg concentrations. Geometric mean blood Hg concentrations were significantly greater in Catskill nestlings (0.78 µg/g ww) than in those from the rest of NY (0.32 µg/g). Mercury concentrations in nestling breast feathers and especially blood samples from the Delaware–Catskill region were generally greater than those reported for most populations sampled elsewhere, including areas associated with significant Hg pollution problems. Bald eagles can serve as valuable Hg bioindicators in aquatic ecosystems of NYS, particularly given their broad statewide distribution and their tendency to nest across all major watersheds and different habitat types.

Epigenetic modifications play an important role in prostate tumor development and progression. Epigenetic drugs are emerging as effective modulators of gene expression that act on pathways potentially important in the control of cancer clinically. We investigated two different epigenetic modulating drugs, SP-2509 and JQ1, that target histone lysine demethylase 1 (LSD1), and bromodomain-containing protein (BRD), respectively and their combined effect in three different prostate cancer (PCa) types: 1) androgen receptor (AR)-positive and androgen-sensitive; 2) AR-positive but castration-resistant; and 3) androgen-nonresponsive. We found combined treatment provided a synergistic growth inhibition in castration-resistant PCa cells but knockdown of AR reduced sensitivity to both inhibitors in these cells. In the androgen-sensitive cell lines, AR knockdown attenuated sensitivity to the LSD1 inhibitor but not the JQ1 inhibitor. Strikingly, treatment with SP-2509 slightly, and JQ1 markedly increased invasion in PCa cells with high AR expression but decreased invasion in PCa cells with low/negative AR expression. Our results suggest that these two epigenetic drugs are novel and promising compounds for the development of PCa therapeutics, particularly for castration-resistant disease. However, due to the potential risks, including metastasis, caution must be exercised in the clinical setting.

Background and AimsImproved modelling of carbon assimilation and plant growth to low soil moisture requires evaluation of underlying mechanisms in the soil, roots, and shoots. The feedback between plants and their local environment throughout the whole spectrum soil-root-shoot-environment is crucial to accurately describe and evaluate the impact of environmental changes on plant development. This study presents a 3D functional structural plant model, in which shoot and root growth are driven by radiative transfer, photosynthesis, and soil hydrodynamics through different parameterisation schemes relating soil water deficit and carbon assimilation. The new coupled model is used to evaluate the impact of soil moisture availability on plant productivity for two different groups of flowering plants under different spatial configurations.MethodsIn order to address different aspects of plant development due to limited soil water availability, a 3D FSP model including root, shoot, and soil was constructed by linking three different well-stablished models of airborne plant, root architecture, and reactive transport in the soil. Different parameterisation schemes were used in order to integrate photosynthetic rate with root water uptake within the coupled model. The behaviour of the model was assessed on how the growth of two different types of plants, i.e. monocot and dicot, is impacted by soil water deficit under different competitive conditions: isolated (no competition), intra, and interspecific competition.Key ResultsThe model proved to be capable of simulating carbon assimilation and plant development under different growing settings including isolated monocots and dicots, intra, and interspecific competition. The model predicted that (1) soil water availability has a larger impact on photosynthesis than on carbon allocation; (2) soil water deficit has an impact on root and shoot biomass production by up to 90 % for monocots and 50 % for dicots; and (3) the improved dicot biomass production in interspecific competition was highly related to root depth and plant transpiration.ConclusionsAn integrated model of 3D shoot architecture and biomass development with a 3D root system representation, including light limitation and water uptake considering soil hydraulics, was presented. Plant-plant competition and regulation on stomatal conductance to drought were able to be predicted by the model. In the cases evaluated here, water limitation impacted plant growth almost 10 times more than the light environment.