nils-herrmann/clean_scirepeval huggingface dataset:
Distinctive Activation Mechanism for Angiotensin Receptor Revealed by a Synthetic Nanobody
Venue: Cell

The angiotensin II (AngII) type 1 receptor (AT1R) is a critical regulator of cardiovascular and renal function and is an important model for studies of G-protein-coupled receptor (GPCR) signaling. By stabilizing the receptor with a single-domain antibody fragment ("nanobody") discovered using a synthetic yeast-displayed library, we determined the crystal structure of active-state human AT1R bound to an AngII analog with partial agonist activity. The nanobody binds to the receptor's intracellular transducer pocket, stabilizing the large conformational changes characteristic of activated GPCRs. The peptide engages the AT1R through an extensive interface spanning from the receptor core to its extracellular face and N terminus, remodeling the ligand-binding cavity. Remarkably, the mechanism used to propagate conformational changes through the receptor diverges from other GPCRs at several key sites, highlighting the diversity of allosteric mechanisms among GPCRs. Our structure provides insight into how AngII and its analogs stimulate full or biased signaling, respectively.
Angiotensin Analogs with Divergent Bias Stabilize Distinct Receptor Conformations
Venue: Cell

"Biased" G protein-coupled receptor (GPCR) agonists preferentially activate pathways mediated by G proteins or β-arrestins. Here, we use double electron-electron resonance spectroscopy to probe the changes that ligands induce in the conformational distribution of the angiotensin II type I receptor. Monitoring distances between 10 pairs of nitroxide labels distributed across the intracellular regions enabled mapping of four underlying sets of conformations. Ligands from different functional classes have distinct, characteristic effects on the conformational heterogeneity of the receptor. Compared to angiotensin II, the endogenous agonist, agonists with enhanced Gq coupling more strongly stabilize an "open" conformation with an accessible transducer-binding site. β-arrestin-biased agonists deficient in Gq coupling do not stabilize this open conformation but instead favor two more occluded conformations. These data suggest a structural mechanism for biased ligand action at the angiotensin receptor that can be exploited to rationally design GPCR-targeting drugs with greater specificity of action.
Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation
Venue: Cell

T helper type 2 (Th2) cells are important regulators of mammalian adaptive immunity and have relevance for infection, autoimmunity, and tumor immunology. Using a newly developed, genome-wide retroviral CRISPR knockout (KO) library, combined with RNA-seq, ATAC-seq, and ChIP-seq, we have dissected the regulatory circuitry governing activation and differentiation of these cells. Our experiments distinguish cell activation versus differentiation in a quantitative framework. We demonstrate that these two processes are tightly coupled and are jointly controlled by many transcription factors, metabolic genes, and cytokine/receptor pairs. There are only a small number of genes regulating differentiation without any role in activation. By combining biochemical and genetic data, we provide an atlas for Th2 differentiation, validating known regulators and identifying factors, such as Pparg and Bhlhe40, as part of the core regulatory network governing Th2 helper cell fates.
Circulating Tumor Cell Clustering Shapes DNA Methylation to Enable Metastasis Seeding
Venue: Cell

The ability of circulating tumor cells (CTCs) to form clusters has been linked to increased metastatic potential. Yet biological features and vulnerabilities of CTC clusters remain largely unknown. Here, we profile the DNA methylation landscape of single CTCs and CTC clusters from breast cancer patients and mouse models on a genome-wide scale. We find that binding sites for stemness- and proliferation-associated transcription factors are specifically hypomethylated in CTC clusters, including binding sites for OCT4, NANOG, SOX2, and SIN3A, paralleling embryonic stem cell biology. Among 2,486 FDA-approved compounds, we identify Na+/K+ ATPase inhibitors that enable the dissociation of CTC clusters into single cells, leading to DNA methylation remodeling at critical sites and metastasis suppression. Thus, our results link CTC clustering to specific changes in DNA methylation that promote stemness and metastasis and point to cluster-targeting compounds to suppress the spread of cancer.
Native American Genomic Diversity through Ancient DNA
Venue: Cell

(; November 15, 2018) In Figure 1 as originally published, the labels indicating Anc-A and Anc-B were inadvertently switched. Anc-A is the origin of the ancestry that spread southward through Central and South America, so this label should appear on the right side of the figure rather than the left. This has now been corrected online, and the authors apologize for any inconvenience.
CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification
Venue: Cell

The ability to engineer natural proteins is pivotal to a future, pragmatic biology. CRISPR proteins have revolutionized genome modification, yet the CRISPR-Cas9 scaffold is not ideal for fusions or activation by cellular triggers. Here, we show that a topological rearrangement of Cas9 using circular permutation provides an advanced platform for RNA-guided genome modification and protection. Through systematic interrogation, we find that protein termini can be positioned adjacent to bound DNA, offering a straightforward mechanism for strategically fusing functional domains. Additionally, circular permutation enabled protease-sensing Cas9s (ProCas9s), a unique class of single-molecule effectors possessing programmable inputs and outputs. ProCas9s can sense a wide range of proteases, and we demonstrate that ProCas9 can orchestrate a cellular response to pathogen-associated protease activity. Together, these results provide a toolkit of safer and more efficient genome-modifying enzymes and molecular recorders for the advancement of precision genome engineering in research, agriculture, and biomedicine.
Bacteria-to-Human Protein Networks Reveal Origins of Endogenous DNA Damage
Venue: Cell

DNA damage provokes mutations and cancer and results from external carcinogens or endogenous cellular processes. However, the intrinsic instigators of endogenous DNA damage are poorly understood. Here, we identify proteins that promote endogenous DNA damage when overproduced: the DNA "damage-up" proteins (DDPs). We discover a large network of DDPs in Escherichia coli and deconvolute them into six function clusters, demonstrating DDP mechanisms in three: reactive oxygen increase by transmembrane transporters, chromosome loss by replisome binding, and replication stalling by transcription factors. Their 284 human homologs are over-represented among known cancer drivers, and their RNAs in tumors predict heavy mutagenesis and a poor prognosis. Half of the tested human homologs promote DNA damage and mutation when overproduced in human cells, with DNA damage-elevating mechanisms like those in E. coli. Our work identifies networks of DDPs that provoke endogenous DNA damage and may reveal DNA damage-associated functions of many human known and newly implicated cancer-promoting proteins.
Activated PMN Exosomes: Pathogenic Entities Causing Matrix Destruction and Disease in the Lung
Venue: Cell

Here, we describe a novel pathogenic entity, the activated PMN (polymorphonuclear leukocyte, i.e., neutrophil)-derived exosome. These CD63+/CD66b+ nanovesicles acquire surface-bound neutrophil elastase (NE) during PMN degranulation, NE being oriented in a configuration resistant to α1-antitrypsin (α1AT). These exosomes bind and degrade extracellular matrix (ECM) via the integrin Mac-1 and NE, respectively, causing the hallmarks of chronic obstructive pulmonary disease (COPD). Due to both ECM targeting and α1AT resistance, exosomal NE is far more potent than free NE. Importantly, such PMN-derived exosomes exist in clinical specimens from subjects with COPD but not healthy controls and are capable of transferring a COPD-like phenotype from humans to mice in an NE-driven manner. Similar findings were observed for another neutrophil-driven disease of ECM remodeling (bronchopulmonary dysplasia [BPD]). These findings reveal an unappreciated role for exosomes in the pathogenesis of disorders of ECM homeostasis such as COPD and BPD, providing a critical mechanism for proteolytic damage.
Biological Functions of Autophagy Genes: A Disease Perspective
Venue: Cell

The lysosomal degradation pathway of autophagy plays a fundamental role in cellular, tissue, and organismal homeostasis and is mediated by evolutionarily conserved autophagy-related (ATG) genes. Definitive etiological links exist between mutations in genes that control autophagy and human disease, especially neurodegenerative, inflammatory disorders and cancer. Autophagy selectively targets dysfunctional organelles, intracellular microbes, and pathogenic proteins, and deficiencies in these processes may lead to disease. Moreover, ATG genes have diverse physiologically important roles in other membrane-trafficking and signaling pathways. This Review discusses the biological functions of autophagy genes from the perspective of understanding-and potentially reversing-the pathophysiology of human disease and aging.
GABAAR Modulator for Postpartum Depression
Venue: Cell

During the postpartum period, the brain's inhibitory GABAA receptors may not recover in time following their reduced numbers during pregnancy. This is likely the cause of postpartum depression prevalent in ∼12% of childbearing women. A new therapy for this condition consists of administering a synthetic neurosteroid during the postpartum period to alleviate the mood disorder. To view this Bench to Bedside, open or download the PDF.
Late Endosomes Act as mRNA Translation Platforms and Sustain Mitochondria in Axons
Venue: Cell

Local translation regulates the axonal proteome, playing an important role in neuronal wiring and axon maintenance. How axonal mRNAs are localized to specific subcellular sites for translation, however, is not understood. Here we report that RNA granules associate with endosomes along the axons of retinal ganglion cells. RNA-bearing Rab7a late endosomes also associate with ribosomes, and real-time translation imaging reveals that they are sites of local protein synthesis. We show that RNA-bearing late endosomes often pause on mitochondria and that mRNAs encoding proteins for mitochondrial function are translated on Rab7a endosomes. Disruption of Rab7a function with Rab7a mutants, including those associated with Charcot-Marie-Tooth type 2B neuropathy, markedly decreases axonal protein synthesis, impairs mitochondrial function, and compromises axonal viability. Our findings thus reveal that late endosomes interact with RNA granules, translation machinery, and mitochondria and suggest that they serve as sites for regulating the supply of nascent pro-survival proteins in axons.
The effects of dissolved oxygen levels on the metabolic interaction between digestion and locomotion in Cyprinid fishes with different locomotive and digestive performances
Venue: Journal of Comparative Physiology B

To test whether the effects of water oxygen concentration ([O2]) on the metabolic interaction between locomotion and digestion differ between fish species with different locomotive and digestive behaviours in normoxia, we investigated the swimming performance of fasted and fed fish at water [O2] of 1, 2 and 8 (normoxia) mg L−1 (2.5, 5 and 20 kPa) at 25°C in three juvenile Cyprinidae fish species: goldfish (Carassius auratus), common carp (Cyprinus carpio) and qingbo (Spinibarbus sinensis). Digestion, taxon and water [O2] all had significant effects on the pre-exercise oxygen consumption rate $$ (\dot{M}{\text{O}}_{{ 2 {\text{pre-exercise}}}} ) $$ and the swimming performance (P < 0.05). Among the three fishes, qingbo showed the highest swimming performance and the lowest feeding $$ \dot{M}{\text{O}}_{2} $$ at the saturated water [O2], and its active oxygen consumption rate $$ (\dot{M}{\text{O}}_{{ 2 {\text{active}}}} ) $$ and critical swimming speed (Ucrit) decreased the most with decreases in water [O2]. Qingbo exhibited a locomotion-priority metabolic mode at all three water [O2]. Digestion was sacrificed to locomotion in a postprandial swimming situation, but fed qingbo could not maintain their Ucrit at water [O2] of 2 and 1 mg L−1. Goldfish showed the lowest swimming performance and the highest feeding $$ \dot{M}{\text{O}}_{2} $$ at the saturated water [O2]. They exhibited a digestion-priority metabolic mode at high water [O2]. However, with a decrease in water [O2], the feeding $$ \dot{M}{\text{O}}_{2} $$ decreased more acutely than the respiratory capacity; thus, digestion and locomotion performed independently in a postprandial swimming situation (i.e., an additive metabolic mode) at a water [O2] of 1 mg L−1. The common carp showed moderate and balanced swimming performance and feeding $$ \dot{M}{\text{O}}_{2} $$ at the saturated water [O2], and exhibited an additive metabolic mode at all 3 water [O2], because digestion, swimming and respiratory capacities decreased in parallel with the decrease in water [O2].
The evolution of mammalian body temperature: the Cenozoic supraendothermic pulses
Venue: Journal of Comparative Physiology B

In this study, I investigated the source(s) of variation in the body temperatures of mammals. I also attempted to reconstruct ancestral normothermic rest-phase body temperature states using a maximum parsimony approach. Body temperature at the familial level is not correlated with body mass. For small mammals, except the Macroscelidae, previously identified correlates, such as climate adaptation and zoogeography explained some, but not all, Tb apomorphies. At the species level in large cursorial mammals, there was a significant correlation between body temperature and the ratio between metatarsal length and femur length, the proxy for stride length and cursoriality. With the exception of two primate families, all supraendothermic (Tb > 37.9°C) mammals are cursorial, including Artiodactyla, Lagomorpha, some large Rodentia, and Carnivora. The ruminant supraendothermic cursorial pulse is putatively associated with global cooling and vegetation changes following the Paleocene–Eocene Thermal Maximum. Reconstructed ancestral body temperatures were highly unrealistic deep within the mammalian phylogeny because of the lack of fossil Tb data that effectively creates ghost lineages. However, it is anticipated that the method of estimating body temperature from the abundance of 13C–18O bonds in the carbonate component of tooth bioapatite in both extant and extinct animals may be a very promising tool for estimating the Tb of extinct mammals. Fossil Tb data are essential for discerning derived Tb reversals from ancestral states, and verifying the dates of supraendothermic pulses.
Benefits of thermal acclimation in a tropical aquatic ectotherm, the Arafura filesnake, Acrochordus arafurae
Venue: Journal of Comparative Physiology B

The presumption that organisms benefit from thermal acclimation has been widely debated in the literature. The ability to thermally acclimate to offset temperature effects on physiological function is prevalent in ectotherms that are unable to thermoregulate year-round to maintain performance. In this study we examined the physiological and behavioural consequences of long-term exposure to different water temperatures in the aquatic snake Acrochordus arafurae. We hypothesised that long dives would benefit this species by reducing the likelihood of avian predation. To achieve longer dives at high temperatures, we predicted that thermal acclimation of A. arafurae would reduce metabolic rate and increase use of aquatic respiration. Acrochordus arafurae were held at 24 or 32°C for 3 months before dive duration and physiological factors were assessed (at both 24 and 32°C). Although filesnakes demonstrated thermal acclimation of metabolic rate, use of aquatic respiration was thermally independent and did not acclimate. Mean dive duration did not differ between the acclimation groups at either temperature; however, warm-acclimated animals increased maximum and modal dive duration, demonstrating a longer dive duration capacity. Our study established that A. arafurae is capable of thermal acclimation and this confers a benefit to the diving abilities of this snake.
Regulation of somatic growth and gene expression of the GH–IGF system and PRP-PACAP by dietary lipid level in early juveniles of a teleost fish, the pejerrey (Odontesthes bonariensis)
Venue: Journal of Comparative Physiology B

Growth and mRNA levels of the pituitary adenylate cyclase-activating polypeptide (PACAP) and its related peptide (PRP), and the system controlled by the growth hormone (GH) and insulin-like growth factors (IGFs) were analyzed in pejerrey fry fed with graded levels of dietary lipids: 10% (L10), 13% (L13) and 21% (L21). First, the full sequence of pejerrey PRP-PACAP was obtained by RT-PCR, using primers based on conserved fragments of teleosts PACAP sequences. The growth of the fish at 83 days after hatching (dah) and the GH mRNA levels were not significantly affected by the dietary treatment. Conversely, PRP-PACAP expression significantly decreased with increasing dietary lipids (L10 > L21). While GH receptor (GHR)-I and IGF-I transcripts did not differ among groups, GHR-II transcripts decreased in group L21. IGF-II expression apparently followed the same trend. These results in combination with the lower expression of the anorexigenic PRP-PACAP in fish fed diet L21 and the correlation analysis evidencing a particularly fine tuning of the GH–IGF system in group L13, suggest that this diet may cover the energy demands for growing pejerrey from 27 dah onwards. Our results show for first time in fish a differential response of PRP-PACAP transcripts to dietary manipulations, and confirm the sensitivity of the pejerrey GH–IGF system to changes in diet composition despite the lack of (or in advance to) a clear response of somatic growth.
Use of bilateral information to determine the walking direction during orientation to a pheromone source in the silkmoth Bombyx mori
Venue: Journal of Comparative Physiology A

Odor source localization is an important animal behavior. Male moths locate mates by tracking sex pheromone emitted by conspecific females. During this type of behavior, males exhibit a combination of upwind surge and zigzagging flight. Similarly, the male walking moth Bombyx mori responds to transient pheromone exposure with a surge in movement, followed by sustained zigzagging walking. The initial surge direction is known to be influenced by the pheromone input pattern. Here, we identified the sensory input patterns that determine the initial walking direction of males. We first quantified the stimulus by measuring electroantennogram values, which were used as a reference for subsequent tests. We used a brief stimulus pulse to examine the relationship between sensory stimulus patterns and the turning direction of initial surge. We found that the difference in input timing and intensity between left and right antennae affected the walking direction, indicating that B. mori integrate bilateral pheromone information during orientation behavior. When we tested pheromone stimulation for longer periods, turning behavior was suppressed, which was induced by stimulus cessation. This study contributes toward understanding efficient strategies for odor-source localization that is utilized by walking insects.
Regulation of nutrient intake in nectar-feeding birds: insights from the geometric framework
Venue: Journal of Comparative Physiology B

A nectar diet is simple in nutritional composition and easily digested, but may vary greatly in its proportions of sugar and water. Here, we apply the geometric framework, a modelling approach for investigating how animals balance nutrient needs in multidimensional and dynamic nutritional environments, to captive whitebellied sunbirds (Cinnyris talatala). We address the question of how these small birds (~8 g) prioritise sugar and water intake, and how dietary salt content interacts with sugar and water intake. Sunbirds kept at 20°C and provided with moderate to high sucrose concentrations (≥1 M), together with supplementary water, converge on an intake target of 2.79 g day−1 of sucrose and 7.72 g day−1 of water: equivalent to 0.85 M sucrose. When the birds are given more dilute sucrose concentrations, they defend their sugar intake by over-ingesting water, up to a ceiling of 47 g day−1. Sugar intake thus gets priority over water intake, but the birds have a finite capacity to over-ingest water to gain the target level of sugar. Regulation appears to be less precise when birds are given a choice between two sucrose solutions than when they choose between a sugar solution and supplementary water. Intake targets vary in response to internal and external factors, and sunbirds increase their sugar intake in response to increased activity and cold, irrespective of nectar concentration. They also compensate for interruptions in foraging activity, whether overnight or during the day. Interactive effects become evident when sodium is included as a third nutrient: on very dilute nectar (≤0.1 M), where sunbirds lose body mass, the addition of sodium to the diet helps to achieve the carbohydrate intake target, while raising the ceiling on water intake. This analysis provides a new perspective on nectarivory, while adding to the comparative database on nutrient regulation and emphasising water as a nutrient.
Glucose and lipid metabolism in the pancreas of rainbow trout is regulated at the molecular level by nutritional status and carbohydrate intake
Venue: Journal of Comparative Physiology B

Glucose and lipid metabolism in pancreatic islet organs is poorly characterized. In the present study, using as a model the carnivorous rainbow trout, a glucose-intolerant fish, we assessed mRNA expression levels of several genes involved in glucose and lipid metabolism (including ATP-citrate lyase; carnitine palmitoyltransferase-1 isoforms, CPT; the mitochondrial isoform of the phosphoenolpyrutave carboxykinase, mPEPCK and pyruvate kinase, PK) and glucosensing (glucose transporter type 2, Glut2; glucokinase, GK and the potassium channel, KATP) in Brockmann bodies. We evaluated the response of these parameters to changes in feeding status (food deprived vs. fed fish) as well as to changes in the amount of carbohydrate (dextrin) in the diet. A general inhibition of the glycolytic (including the glucosensing marker GK) and β-oxidation pathways was found when comparing fed versus food-deprived fish. When comparing fish feeding on either low- or high-carbohydrate diets, we found that some genes related to lipid metabolism were more controlled by the feeding status than by the carbohydrate content (fatty acid synthase, CPTs). Findings are discussed in the context of pancreatic regulation of glucose and lipid metabolism in fish, and show that while trout pancreatic metabolism can partially adapt to a high-carbohydrate diet, some of the molecular actors studied seem to be poorly regulated (KATP) and may contribute to the glucose intolerance observed in this species when fed high-carbohydrate diets.