Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanistic Insights into pH‐sensing GPCRs

Many aspects of protein function, cell biology, human physiology, and disease are influenced by pH changes. However, our mechanistic understanding of pH effects in most of these areas is limited. This is especially true in the case of cell signaling, for which very few pH‐sensing receptors and signaling cascades have been identified. To address this issue, we are studying how pH regulates G protein‐coupled receptors (GPCRs), the largest and most therapeutically targeted family of cell‐surface receptors in humans. Unlike most cellular proteins, GPCRs are regularly exposed to a wide range of dynamic pH values (from pH 7.4 on the cell surface, to pH 5.0 in endosomes) and can be chronically exposed to acidic microenvironments caused by cancer and processes such as inflammation. While there are more than 800 GPCR family members, only three receptors (i.e. GPR4, GPR65, and GPR68) are known to be activated directly by pH. In this study, we used structural informatics and cell‐based signaling assays to predict and validate residues responsible for pH sensing by these receptors. As part of these efforts, we engineered and interrogated 44 GPR4, GPR65, and GPR68 point mutations in a library of 440 cell strains that covered all possible GPCR‐Gα subunit signaling combinations. This comprehensive strain library included 14 mutations predicted by our structural informatics software, pHinder, and the full set of 30 mutations for these receptors available in the literature. Our results for the known mutants agree with previous reports and expand our understanding of the relationship between Gα‐signaling specificity and pH sensing. More importantly, several of our newly predicted mutations appear to have a greater influence on the pH‐sensing capabilities of these receptors than any of the previously reported GPR4, GPR65, and GPR68 mutations to date. Most of the pH‐sensitive residues predicted by pHinder were found within the protein core, a region that has been largely overlooked when considering pH‐sensing properties of GPCRs. Our cell‐based experiments confirmed that these residues are critical for pH sensing and provide a more thorough knowledge‐base for understanding GPCR pH sensing. We anticipate that the outcome of these studies will enable us to more comprehensively quantify the extent of pH sensing across the GPCRome and rationally engineer new pH‐sensing GPCRs for use in industry, synthetic biology, and medicine.
Hydraulic Conductance and Xylem Anatomy in Fruit Tree Shoots

Hydraulic conductance is an important index of water flow in plants. We constructed a simple device for measuring the relative hydraulic conductance of fruit tree shoots. The values of vines (kiwifruit and grape) were the highest among 17 species of major temperate fruit trees, followed by deciduous trees (e.g. chestnut, Japanese pear, and peach), evergreen citrus trees (e.g. Kawanonatsudaidai and Satsuma mandarin), and loquat. The diameter and number of vessels and total vessel area in shoots were calculated with image analysis software from photomicrographs of 13 of the species. The diameter of the vessels was largest in vines (kiwifruit and grape), followed by persimmon and chestnut, and smallest in deciduous trees (e.g. apple and Japanese apricot), citrus, and loquat. Relative hydraulic conductance had a higher correlation with the water flow index (Σr4/S × (xylem ratio)), calculated from the diameter and number of vessels in the xylem according to the Hagen–Poiseuille law, and than with total vessel area per unit of shoot cross-sectional area.
Regulatory Role of Ceramide/mTOR Signaling in Exosome Secretion from Smooth Muscle Cells during Arterial Stiffening and Medial Calcification

Increased secretion of exosomes from arterial smooth muscle cells (SMCs) has been shown to contribute to arterial medial calcification (AMC) associated with accumulation of calcium deposits in the arterial wall and osteoblastic differentiation of SMCs. In this study, we further explored the molecular mechanisms increasing exosome secretion during AMC, focusing on lysosomal‐ceramide/mTOR (mammalian target of rapamycin) signaling in the regulation of lysosome trafficking and exosome release. Smooth muscle‐specific lysosomal acid ceramidase (Ac) gene knock out (Asah1fl/fl/SMcre) mice were treated with a high dose of Vit D (500,000 IU/kg/day) for 4 days. By Alizarin Red S and Von Kossa staining, we observed significantly increased aortic medial calcification with augmented expression of osteogenic markers like osteopontin and RUNX2 in Asah1fl/fl/SMcre mice compared to their wild type littermates, which was markedly attenuated by pretreatment of these mice with Torin‐1, an mTOR inhibitor. Confocal microscopy showed Asah1fl/fl/SMcre mice had markedly increased colocalization of mTORC1 with Lamp‐1(lysosome marker), but decreased colocalization of VPS16 (a multivesicular bodies (MVBs) marker) with Lamp‐1, suggesting mTOR activation and reduced MVBs interaction with lysosomes. However, mTOR inhibition by Torin‐1 significantly reduced the colocalization of mTOR vs Lamp‐1 which inturn increased lysosome‐MVBs interaction. Torin‐1 was also found to reduce accumulation of CD63 and annexin 2 (AnX2) (exosome markers) in the coronary arterial wall of Asah1fl/fl/SMcre mice compared to wild type littermates. Using CASMCs, we observed that Ac gene deletion led to peripheral distribution of lysosomes and increased exosome secretion, which was blocked by Torin‐1. Functionally, Torin‐1 was found to significantly reduce arterial stiffening Asah1fl/fl/SMcre mice as shown by restoration from increased pulse wave velocity (PWV). Altogether, these results suggest that lysosomal ceramide‐mTOR signaling is critical for the control of lysosome trafficking, exosome secretion and arterial stiffening or osteogenesis.
Effects of Wen‐Pi‐Tang and its crude drug extracts on proliferation of cultured mouse mesangial cells

The efficacy of Wen‐Pi‐Tang and each of its crude drug extracts on the proliferation of mouse mesangial cells was determined in terms of [3H]thymidine uptake. When Wen‐Pi‐Tang was added to the medium of mesangial cell cultures, it suppressed the proliferation of mesangial cells markedly. Similar to the effects of Wen‐Pi‐Tang, Rhei Rhizoma, its main ingredient, exerted an inhibitory effect on mesangial cell proliferation at a relatively low concentration. Ginseng Radix and Aconiti Tuber were also an effective crude drug. As for Zingiberis Rhizoma, an inhibitory activity at relatively high concentration was noted. However, the proliferation of mesangial cells in the presence of Glycyrrhizae Radix showed no particular alteration. As is clear from the results of the present study, Rhei Rhizoma, Ginseng Radix, Aconiti Tuber and Zingiberis Rhizoma alone each exert an inhibitory effect. The inhibition of mesangial cell proliferation by Wen‐Pi‐Tang can thus be explained by the action of these crude drugs.
Allozyme and mitochondrial DNA separation of Pacific northern bluefin tuna, Thunnus thynnus orientalis (Temminck and Schlegel), from southern bluefin tuna, Thunnus maccoyii (Castelnau)

Northern and southern bluefin tunas are morphologically similar and can be misidentified, posing problems for fishery management and marketing. Allozyme variation and restriction-site variation in mitochondrial DNA (mtDNA) were used to distinguish between the two species. A survey of 36 allozyme loci active in white muscle and liver tissue showed that the genetic identity between the species was high (Nei's I = 0.907). One diagnostic locus (sAH*) and two nearly diagnostic loci (ADA* and GDA*) were found, and four loci showed highly significant allele frequency differences (FH*, GPI-A*, PGDH* and sSOD*). A survey of the mtDNA genome, using 15 restriction enzymes and southern blotting, revealed five restriction enzymes that gave species-diagnostic restriction digest profiles (Ban I, Bcl I, Dra I, Pvu II, Xba I) and a further three enzymes (Pst I, Barn HI and Nco I) with large haplotype frequency differences. Mitochondrial DNA analysis provided more reliable discrimination of specimens than did allozyme analysis, although the more rapid allozyme identification will be accurate for most specimens. The two biochemical genetic methods were then used to identify Australian-caught fish of uncertain identity. Six of 12 tuna originally considered to be northern bluefin tuna were confirmed as northern bluefin and six were identified as southern bluefin. The presence of northern bluefin tuna as far south as south-western Tasmania was confirmed.
DSCAM-AS1-Driven Proliferation of Breast Cancer Cells Involves Regulation of Alternative Exon Splicing and 3′-End Usage

DSCAM-AS1 is a cancer-related long noncoding RNA with higher expression levels in Luminal A, B, and HER2-positive Breast Carcinoma (BC), where its expression is strongly dependent on Estrogen Receptor Alpha (ERα). DSCAM-AS1 expression is analyzed in 30 public datasets and, additionally, by qRT-PCR in tumors from 93 BC patients, to uncover correlations with clinical data. Moreover, the effect of DSCAM-AS1 knockdown on gene expression and alternative splicing is studied by RNA-Seq in MCF-7 cells. We confirm DSCAM-AS1 overexpression in high grade Luminal A, B, and HER2+ BCs and find a significant correlation with disease relapse. In total, 908 genes are regulated by DSCAM-AS1-silencing, primarily involved in the cell cycle and inflammatory response. Noteworthily, the analysis of alternative splicing and isoform regulation reveals 2085 splicing events regulated by DSCAM-AS1, enriched in alternative polyadenylation sites, 3′UTR (untranslated region) shortening and exon skipping events. Finally, the DSCAM-AS1-interacting splicing factor heterogeneous nuclear ribonucleoprotein L (hnRNPL) is predicted as the most enriched RBP for exon skipping and 3′UTR events. The relevance of DSCAM-AS1 overexpression in BC is confirmed by clinical data and further enhanced by its possible involvement in the regulation of RNA processing, which is emerging as one of the most important dysfunctions in cancer.
Evolutionary Assurance vs. Mixed Mating

Reproductive assurance is a widely accepted explanation for the evolution of selfing, although theory suggests that an evolutionarily stable mixed mating strategy does not maximize seed production. We present a correlation analysis involving 28 species representing 23 families showing that selfing can evolve independently of inbreeding depression. We discuss the cost-benefit trade-off of selfing, in particular the incongruence of whether delayed selfing provides reproductive assurance in 22 species representing 14 families, in which pollen and seed discounting are minimized when pollinators or mates are scarce. Reproductive assurance, in response to frequent pollinator failure, can be reconciled with an evolutionarily stable mixed mating system contributed to by delayed selfing, which is still advantageous even if there is strong inbreeding depression.
Preening, plumage reflectance and female choice in budgerigars

Plumage ornaments are important signals in sexual selection context. Plumage maintenance is therefore important not only for insulation and flight but also for ornament efficacy. However, the effect of plumage maintenance on ornament characteristics and female choice has never been investigated experimentally. In this study we focused on the influence of preening on plumage reflectance and, indirectly, on female preference in the budgerigar Melopsittacus undulatus. We measured the effect of preening on the reflectance of previously soiled plumage. Our results suggest that soiling affects plumage reflectance in budgerigars that are prevented from preening and that this effect is particularly pronounced in the UV range. In contrast, individuals that were allowed to preen restored their plumage reflectance spectrum to presoiling levels. In a two-choice test, females presented with clean (preened) and soiled (unpreened) males, spent more time near the clean male. These results suggest that female budgerigars are able to discriminate between preened and unpreened males. Further investigations, conducted under various soiling conditions, are necessary to confirm the effect of soiling on plumage reflectance spectrum and to investigate which cues are used by females to discriminate between preened and unpreened males. Such research could reveal whether UV feather ornaments, mediated by preening, are special signals conveying information about a bird's current condition.
Coupling law enforcement and community-based regulations in support of compliance with biodiversity conservation regulations

Summary The scope and scale of wildlife crimes around the world have risen in intensity and complexity, yet current enforcement strategies have often not delivered desired effects on illegal activities, even within protected areas. Tackling the array of illegal activities by emphasizing law enforcement above other options is challenging and potentially unsustainable. We explored the potential for social norms, community regulations and socioeconomic factors to promote compliance with wildlife laws by interviewing 334 respondents in 28 villages that share boundaries with protected areas in Nigeria. Using an anonymous direct questioning approach, we recorded a high prevalence of non-compliance behaviours in all studied communities. Injunctive norms (i.e., perceptions of acceptable behaviour within a social group) significantly predicted compliance, as respondents with no complicit friends or family members were more likely to comply with wildlife regulations. Perceived likelihood of community-level sanctions played a more salient role than the fear of arrest by rangers in influencing compliance. In addition, non-compliance increased with number of dependents, but reduced with average monthly household income. Our study demonstrates that clear knowledge of the social norms that drive local behaviour as well as the authorities that enforce them is integral to understanding the forces that drive community involvement and participation in conservation. Incorporating local communities in planning enforcement interventions may help protect threatened species and landscapes.
Innovative approach to a functional mediastinal paraganglioma with anomalous coronary supply: a case report

Abstract Background Mediastinal paragangliomas (PGs) are rare and particularly challenging neuroendocrine tumours. Clinical presentation is heterogeneous and tumour resection can be challenging due to bleeding and the risk of catecholamine surges in functional tumours. Case Summary A 36-year-old man with multiple cardiovascular risk factors was admitted with subacute heart failure. Investigations revealed a large non-metastatic functional mediastinal PG irrigated mainly by a left circumflex coronary anomalous feeder branch. The surgical risk was deemed very high due to patient comorbidities, tumour vascularization, and close relation to major thoracic structures. A multidisciplinary team decided to perform embolization of the anomalous coronary branch followed by peptide-receptor radionuclide therapy with 177-LuDOTATE aiming to decrease tumour size and perioperative risk. Follow-up studies showed a reduction in tumour vascularization, size, and hormonal production. Discussion The innovative strategy of combining embolization of the anomalous feeder branch with radionuclide therapy proved to be a promising approach.
Lipid Droplet Proteome Dynamics and Lipotoxicity

Lipid droplets are ER‐derived neutral lipid storage organelles that function as cellular hubs of lipid metabolism, providing an “on demand” source of fatty acids for energy and sequestering fatty acids to protect cells from lipotoxic damage. Lipid droplet functions are controlled by associated integral and peripheral proteins. To understand the composition of lipid droplet proteomes, we recently developed a proximity labeling strategy to define high confidence lipid droplet proteomes. This approach uses lipid droplet‐targeted ascorbate peroxidase (APEX2), which enables the biotinylation of neighboring proteins in a spatially and temporally defined manner. Employing this method, we defined high confidence lipid droplet proteomes in multiple cell lines and identified pathways that impact lipid droplet proteome composition, uncovering a role for a ubiquitin‐dependent ER‐associated degradation (ERAD) pathway in the clearance of select lipid droplet proteins. A key function of lipid droplets is to sequester fatty acids to prevent lipotoxicity. To further understand how the cell responds to lipotoxic insults, we leveraged whole‐genome CRISPR‐Cas9 screens to dissect pathways that regulate lipid damage. For example, exploiting a synthetic lethal screening strategy, we discovered a new pathway that promotes cancer cell resistance to a regulated form of cell death known as ferroptosis, which involves the iron‐dependent accumulation of oxidatively damaged lipids. This study uncovered an unexpected role for non‐mitochondrial CoQ as a lipophilic antioxidant that prevents membrane damage. Together, our findings highlight the integration of systems level discovery approaches and cell biology methods as a powerful strategy to understand the mechanisms that regulate lipid droplets and lipotoxicity.
Dietary self‐selection by Heliothis zea larvae: roles of metabolic feedback and chemosensory stimuli

The effects on dietary self‐selection of phagostimulation and metabolic feedback from nutrients were seperated by using two unusual carbohydrates alone or in combination: mannitol, which is nutritive but not phagostimulatory for H. zea larvae; and sorbose, which is weakly phagostimulatory but not nutritive. Last instar H. zea larvae recognized and responded positively to mannitol by metabolic feedback when it was included in a diet with casein. When offered a choice of two diets, one containing casein but lacking a utilizable carbohydrate and another lacking casein but including either mannitol or sorbose, they did not self‐select for either mannitol or sorbose. However, in a similar experiment, in which the carbohydrate diet contained a mixture of mannitol and sorbose, there was a positive response, demonstrating that both metabolic feedback and phagostimulation are required to elicit self‐selection.
The Modes of Cell Death Induced by PDT: An Overview

Summary Photodynamic therapy (PDT) is a relatively new treatment for malignant and non-malignant diseases and by now successfully employed in many clinical applications. It is typically carried out as a two-step protocol with target cells first being selectively loaded with a photosensitizer followed by irradiation with light of the appropriate wavelength. Subsequent photochemical reactions lead to the production of reactive oxygen species (ROS) and cell death. PDT can trigger both modes of cell death, apoptosis and necrosis in target cells. Apoptosis is an active, controlled and energy-requiring process and therefore contrasts necrosis, which is an entropic event and in most cases a consequence of loss of membrane integrity and metabolic homeostasis. Photodynamic therapy has been shown to effectively induce apoptosis in several model systems since ROS formed by photoprocesses can directly damage mitochondria, which act as key regulators in active cell death. Therefore PDT may be able to set off the apoptotic cascade even in those cells which were shown to be resistant to apoptosis in response to chemotherapy or ionizing radiation. The cell death mode after PDT is of interest since it influences the response of the immune system and therefore the effectiveness of the treatment: apoptotic as well as necrotic cell death influence the activity and the specific response of various cell types involved in potential antitumor response of the immune system. The mode of cell death triggered by PDT can be influenced by altering the treatment protocol and can lead to a desired apoptosis/ necrosis ratio most advantageous for complete tumor eradication.
Long‐term spatial dynamics in vegetated seascapes: fragmentation and habitat loss in a human‐impacted subtropical lagoon

Vegetated coastal seascapes exhibit dynamic spatial patterning, some of which is directly linked to human coastal activities. Human activities (e.g. coastal development) have modified freshwater flow to marine environments, resulting in significant changes to submerged aquatic vegetation (SAV) communities. Yet, very little is known about the spatially complex process of SAV habitat loss and fragmentation that affects ecosystem function. Using habitat mapping from aerial photography spanning 71 years (1938–2009) for Biscayne Bay (Florida, USA), we quantify both SAV habitat loss and fragmentation using a novel fragmentation index. To understand the influence of water management practices on SAV seascapes, habitat loss and fragmentation were compared between nearshore and offshore locations, as well as locations adjacent to and distant from canals that transport freshwater into the marine environment. Habitat loss and fragmentation were significantly higher along the shoreline compared with offshore seascapes. Nearshore habitats experienced a net loss of 3.31% of the total SAV mapped (2.57 km 2 ) over the time series. While areas adjacent to canals had significantly higher SAV cover, they still experienced wide fluctuations in cover and fragmentation over time. All sites exhibited higher fragmentation in 2009 compared with 1938, with four sites exhibiting high fragmentation levels between the 1990s and 2000s. We demonstrate that freshwater inputs into coastal bays modify the amount of SAV and the fragmentation dynamics of SAV habitats. Spatial changes are greater close to shore and canals, indicating that these coastal developments have transformative impacts on vegetated habitats, with undetermined consequences for the provisioning of ecosystem goods and services.
Conservation implications of genetic variation between spatially and temporally distinct colonies of the endangered damselfly Coenagrion mercuriale

Abstract. 1. Good conservation management is underpinned by a thorough understanding of species' historical and contemporary dispersal capabilities along with the possible adaptive or neutral processes behind any spatio‐temporal genetic structuring. These issues are investigated with respect to the rare damselfly Coenagrion mercuriale (Charpentier) – the only odonate species currently listed in the U.K.'s Biodiversity Action Plan – in east Devon where its distribution has become fragmented.
Effects of variations in stand structure on development of mixed-species stands in eastern Washington

The development of six mixed-species, even-aged stands was reconstructed in the eastern Washington Cascade Range. All stands were within the Grand Fir Climax Series and began following stand replacement disturbances. Western larch (Larixoccidentalis Nutt.) and lodgepole pine (Pinuscontorta Dougl. ex Loud.), when present, formed an upper stratum over interior Douglas-fir (Pseudotsugamenziesii var. glauca (Beissn.) Franco) and grand fir (Abiesgrandis (Dougl.) Lindl. ) in all six stands. Establishment patterns and species composition affected stand development patterns. Douglas-fir benefitted from the absence of lodgepole pine; grand fir benefitted from the absence of Douglas-fir, but apparently not from the absence of lodgepole pine. Lodgepole pine had faster initial diameter growth rates than western larch when it became established relatively early and in large numbers.