Miracle-dz/UniFAR-FTUs huggingface dataset:
Adapting North American wheat production to climatic challenges, 1839–2009

The Intergovernmental Panel on Climate Change projects that temperatures in the major grain-growing areas of North America will rise by 3–4 °C by 2100. Such abrupt changes will create major challenges, significantly altering the area suitable for wheat. The historical record offers insight into the capability of agriculture to adapt to climatic challenges. Using a new county-level dataset on wheat production and climate norms, we show that during the 19th and 20th centuries North American grain farmers pushed wheat production into environments once considered too arid, too variable, and too harsh to cultivate. As summary measures, the median annual precipitation norm of the 2007 distribution of North American wheat production was one-half that of the 1839 distribution, and the median annual temperature norm was 3.7 °C lower. This shift, which occurred mostly before 1929, required new biological technologies. The Green Revolution associated with the pioneering work of Norman Borlaug represented an important advance in this longer process of biological innovation. However, well before the Green Revolution, generations of North American farmers overcame significant climatic challenges.
Unconventional myristoylation of large-conductance Ca2+-activated K+ channel (Slo1) via serine/threonine residues regulates channel surface expression

Protein myristoylation is a means by which cells anchor proteins into membranes. The most common type of myristoylation occurs at an N-terminal glycine. However, myristoylation rarely occurs at an internal amino acid residue. Here we tested whether the α-subunit of the human large-conductance voltage- and Ca2+-activated K+ channel (hSlo1) might undergo internal myristoylation. hSlo1 expressed in HEK293T cells incorporated [3H]myristic acid via a posttranslational mechanism, which is insensitive to cycloheximide, an inhibitor of protein biosynthesis. In-gel hydrolysis of [3H]myristoyl-hSlo1 with alkaline NH2OH (which cleaves hydroxyesters) but not neutral NH2OH (which cleaves thioesters) completely removed [3H]myristate from hSlo1, suggesting the involvement of a hydroxyester bond between hSlo1’s hydroxyl-bearing serine, threonine, and/or tyrosine residues and myristic acid; this type of esterification was further confirmed by its resistance to alkaline Tris·HCl. Treatment of cells expressing hSlo1 with 100 μM myristic acid caused alteration of hSlo1 activation kinetics and a 40% decrease in hSlo1 current density from 20 to 12 nA*MΩ. Immunocytochemistry confirmed a decrease in hSlo1 plasmalemma localization by myristic acid. Replacement of the six serines or the seven threonines (but not of the single tyrosine) of hSlo1 intracellular loops 1 and 3 with alanines decreased hSlo1 direct myristoylation by 40–44%, whereas in combination decreased myristoylation by nearly 90% and abolished the myristic acid-induced change in current density. Our data demonstrate that an ion channel, hSlo1, is internally and posttranslationally myristoylated. Myristoylation occurs mainly at hSlo1 intracellular loop 1 or 3, and is an additional mechanism for channel surface expression regulation.
Proinflammatory T helper type 17 cells are effective B-cell helpers

T helper type 17 (TH17) cells are highly proinflammatory effector T cells that are characterized by the production of high amounts of IL-17A, IL-17F, IL-21, and IL-22. Furthermore, TH17 cells have been associated with a number of autoimmune diseases. However, it is not clear whether TH17 cells can also serve as effective helper cells. Here we show that TH17 cells can function as B-cell helpers in that they not only induce a strong proliferative response of B cells in vitro but also trigger antibody production with class switch recombination in vivo. Transfer of TH17 cells into WT or T-cell receptor α–deficient mice, which lack endogenous T cells, induces a pronounced antibody response with preferential isotype class switching to IgG1, IgG2a, IgG2b, and IgG3, as well as the formation of germinal centers. Conversely, blockade of IL-17 signaling results in a significant reduction in both number and size of germinal centers. Whereas IL-21 is known to help B cells, IL-17 on its own drives B cells to undergo preferential isotype class switching to IgG2a and IgG3 subtypes. These observations provide insights into the unappreciated role of TH17 cells and their signature cytokines in mediating B-cell differentiation and class switch recombination.
A context-specific cardiac β-catenin and GATA4 interaction influences TCF7L2 occupancy and remodels chromatin driving disease progression in the adult heart

Abstract Chromatin remodelling precedes transcriptional and structural changes in heart failure. A body of work suggests roles for the developmental Wnt signalling pathway in cardiac remodelling. Hitherto, there is no evidence supporting a direct role of Wnt nuclear components in regulating chromatin landscapes in this process. We show that transcriptionally active, nuclear, phosphorylated(p)Ser675-β-catenin and TCF7L2 are upregulated in diseased murine and human cardiac ventricles. We report that inducible cardiomyocytes (CM)-specific pSer675-β-catenin accumulation mimics the disease situation by triggering TCF7L2 expression. This enhances active chromatin, characterized by increased H3K27ac and TCF7L2 occupancies to cardiac developmental and remodelling genes in vivo. Accordingly, transcriptomic analysis of β-catenin stabilized hearts shows a strong recapitulation of cardiac developmental processes like cell cycling and cytoskeletal remodelling. Mechanistically, TCF7L2 co-occupies distal genomic regions with cardiac transcription factors NKX2–5 and GATA4 in stabilized-β-catenin hearts. Validation assays revealed a previously unrecognized function of GATA4 as a cardiac repressor of the TCF7L2/β-catenin complex in vivo, thereby defining a transcriptional switch controlling disease progression. Conversely, preventing β-catenin activation post-pressure-overload results in a downregulation of these novel TCF7L2-targets and rescues cardiac function. Thus, we present a novel role for TCF7L2/β-catenin in CMs-specific chromatin modulation, which could be exploited for manipulating the ubiquitous Wnt pathway.
RNentropy: an entropy-based tool for the detection of significant variation of gene expression across multiple RNA-Seq experiments

Abstract RNA sequencing (RNA-Seq) has become the experimental standard in transcriptome studies. While most of the bioinformatic pipelines for the analysis of RNA-Seq data and the identification of significant changes in transcript abundance are based on the comparison of two conditions, it is common practice to perform several experiments in parallel (e.g. from different individuals, developmental stages, tissues), for the identification of genes showing a significant variation of expression across all the conditions studied. In this work we present RNentropy, a methodology based on information theory devised for this task, which given expression estimates from any number of RNA-Seq samples and conditions identifies genes or transcripts with a significant variation of expression across all the conditions studied, together with the samples in which they are over- or under-expressed. To show the capabilities offered by our methodology, we applied it to different RNA-Seq datasets: 48 biological replicates of two different yeast conditions; samples extracted from six human tissues of three individuals; seven different mouse brain cell types; human liver samples from six individuals. Results, and their comparison to different state of the art bioinformatic methods, show that RNentropy can provide a quick and in depth analysis of significant changes in gene expression profiles over any number of conditions.
Recognition of tandem PxxP motifs as a unique Src homology 3-binding mode triggers pathogen-driven actin assembly

Src homology 3 (SH3) domains are globular protein interaction modules that regulate cell behavior. The classic SH3 ligand-binding site accommodates a hydrophobic PxxP motif and a positively charged specificity-determining residue. We have determined the NMR structure of insulin receptor tyrosine kinase substrate (IRTKS) SH3 domain in complex with a repeat from Escherichia coli-secreted protein F-like protein encoded on prophage U (EspFU), a translocated effector of enterohemorrhagic E. coli that commandeers the mammalian actin assembly machinery. EspFU-IRTKS interaction is among the highest affinity natural SH3 ligands. Our complex structure reveals a unique type of SH3 interaction based on recognition of tandem PxxP motifs in the ligand. Strikingly, the specificity pocket of IRTKS SH3 has evolved to accommodate a polyproline type II helical peptide analogously to docking of the canonical PxxP by the conserved IRTKS SH3 proline-binding pockets. This cooperative binding explains the high-affinity SH3 interaction and is required for EspFU-IRTKS interaction in mammalian cells as well as the formation of localized actin “pedestals” beneath bound bacteria. Importantly, tandem PxxP motifs are also found in mammalian ligands and have been shown to contribute to IRTKS SH3 recognition similarly.
Regulation of the positive transcriptional effect of PLZF through a non-canonical EZH2 activity

Abstract The transcription factor PLZF (promyelocytic leukemia zinc finger protein) acts as an epigenetic regulator balancing self-renewal and differentiation of hematopoietic cells through binding to various chromatin-modifying factors. First described as a transcriptional repressor, PLZF is also associated with active transcription, although the molecular bases underlying the differences are unknown. Here, we reveal that in a hematopoietic cell line, PLZF is predominantly associated with transcribed genes. Additionally, we identify a new association between PLZF and the histone methyltransferase, EZH2 at the genomic level. We find that co-occupancy of PLZF and EZH2 on chromatin at PLZF target genes is not associated with SUZ12 or trimethylated lysine 27 of histone H3 (H3K27me3) but with the active histone mark H3K4me3 and active transcription. Removal of EZH2 leads to an increase of PLZF binding and increased gene expression. Our results suggest a new role of EZH2 in restricting PLZF positive transcriptional activity independently of its canonical PRC2 activity.
Human La binds mRNAs through contacts to the poly(A) tail

Abstract In addition to a role in the processing of nascent RNA polymerase III transcripts, La proteins are also associated with promoting cap-independent translation from the internal ribosome entry sites of numerous cellular and viral coding RNAs. La binding to RNA polymerase III transcripts via their common UUU-3’OH motif is well characterized, but the mechanism of La binding to coding RNAs is poorly understood. Using electromobility shift assays and cross-linking immunoprecipitation, we show that in addition to a sequence specific UUU-3’OH binding mode, human La exhibits a sequence specific and length dependent poly(A) binding mode. We demonstrate that this poly(A) binding mode uses the canonical nucleic acid interaction winged helix face of the eponymous La motif, previously shown to be vacant during uridylate binding. We also show that cytoplasmic, but not nuclear La, engages poly(A) RNA in human cells, that La entry into polysomes utilizes the poly(A) binding mode, and that La promotion of translation from the cyclin D1 internal ribosome entry site occurs in competition with cytoplasmic poly(A) binding protein (PABP). Our data are consistent with human La functioning in translation through contacts to the poly(A) tail.
Freestanding Mesoporous VN/CNT Hybrid Electrodes for Flexible All‐Solid‐State Supercapacitors

High-performance all-solid-state supercapacitors (SCs) are fabricated based on thin, lightweight, and flexible freestanding MVNN/CNT hybrid electrodes. The device shows a high volume capacitance of 7.9 F/cm(3) , volume energy and power density of 0.54 mWh/cm(3) and 0.4 W/cm(3) at a current density of 0.025 A/cm(3) . By being highly flexible, environmentally friendly, and easily connectable in series and parallel, the all-solid-state SCs promise potential applications in portable/wearable electronics.
Reconstructing a solid-solid phase transformation pathway in CdSe nanosheets with associated soft ligands

Integrated single-crystal-like small and wide-angle X-ray diffraction images of a CdSe nanosheet under pressure provide direct experimental evidence for the detailed pathway of transformation of the CdSe from a wurtzite to a rock-salt structure. Two consecutive planar atomic slips [(001) 〈110〉 in parallel and (102) with a distortion angle of ∼40°] convert the wurtzite-based nanosheet into a saw-like rock-salt nanolayer. The transformation pressure is three times that in the bulk CdSe crystal. Theoretical calculations are in accord with the mechanism and the change in transformation pressure, and point to the critical role of the coordinated amines. Soft ligands not only increase the stability of the wurtzite structure, but also improve its elastic strength and fracture toughness. A ligand extension of 2.3 nm appears to be the critical dimension for a turning point in stress distribution, leading to the formation of wurtzite (001)/zinc-blende (111) stacking faults before rock-salt nucleation.
Ezh2 promotes clock function and hematopoiesis independent of histone methyltransferase activity in zebrafish

Abstract EZH2 is a subunit of polycomb repressive complex 2 (PRC2) that silences gene transcription via H3K27me3 and was shown to be essential for mammalian liver circadian regulation and hematopoiesis through gene silencing. Much less, however, is known about how Ezh2 acts in live zebrafish. Here, we show that zebrafish ezh2 is regulated directly by the circadian clock via both E-box and RORE motif, while core circadian clock genes per1a, per1b, cry1aa and cry1ab are down-regulated in ezh2 null mutant and ezh2 morphant zebrafish, and either knockdown or overexpression of ezh2 alters locomotor rhythms, indicating that Ezh2 is required for zebrafish circadian regulation. In contrast to its canonical silencing function, zebrafish Ezh2 up-regulates these key circadian clock genes independent of histone methyltransferase activity by directly binding to key circadian clock proteins. Similarly, Ezh2 contributes to hematopoiesis by enhancing expression of hematopoietic genes such as cmyb and lck. Together, our findings demonstrate for the first time that Ezh2 acts in both circadian regulation and hematopoiesis independent of silencing PRC2.
Protection against the Extravasation of Anticancer Drugs by Standardization of the Management System

The extravasation of anticancer drugs is a serious complication. On the basis of data regarding extravasation prevention and treatment obtained primarily by pharmacists, the management system for extravasation of anticancer drugs was standardized at an outpatient chemotherapy center. A kit was prepared so that physicians could promptly and safely perform venipuncture; the kit included a classification list of anticancer drugs. Prior to administration of vesicant or irritant drugs, pharmacists and nurses educated the patients. When anticancer drugs were administered via peripheral vein without using an implanted venous access device, extravasation occurred in 10 out of 7,059 courses (0.14%) during the 2-year study period postintroduction of the present management system. This incidence is remarkably low as compared with those previously reported. The extravasated drugs were epirubicin (n = 3), paclitaxel (n = 3), vinorelbine (n = 1), 5–fluorouracil (n = 1), carboplatin (n = 1), and cyclophosphamide (n = 1). Cold packs were applied around the injection site except in the cases involving vinorelbine, in which warm packs were used. In all cases of extravasation of vesicant drugs, glucocorticoid was injected locally. There were no cases involving continuous pain or skin ulcers. The standardization of the management system for extravasation of anticancer drugs was very effective in decreasing the occurrence, as well as decreasing skin damage if it occurred.
Soluble amyloid precursor protein (APP) regulates transthyretin and Klotho gene expression without rescuing the essential function of APP

Amyloidogenic processing of the amyloid precursor protein (APP) generates a large secreted ectodomain fragment (APPsβ), β-amyloid (Aβ) peptides, and an APP intracellular domain (AICD). Whereas Aβ is viewed as critical for Alzheimer's disease pathogenesis, the role of other APP processing products remains enigmatic. Of interest, the AICD has been implicated in transcriptional regulation, and N-terminal cleavage of APPsβ has been suggested to produce an active fragment that may mediate axonal pruning and neuronal cell death. We previously reported that mice deficient in APP and APP-like protein 2 (APLP2) exhibit early postnatal lethality and neuromuscular synapse defects, whereas mice with neuronal conditional deletion of APP and APLP2 are viable. Using transcriptional profiling, we now identify transthyretin (TTR) and Klotho as APP/APLP2-dependent genes whose expression is decreased in loss-of-function states but increased in gain-of-function states. Significantly, by creating an APP knockin allele that expresses only APPsβ protein, we demonstrate that APPsβ is not normally cleaved in vivo and is fully capable of mediating the APP-dependent regulation of TTR and Klotho gene expression. Despite being an active regulator of gene expression, APPsβ did not rescue the lethality and neuromuscular synapse defects of APP and APLP2 double-KO animals. Our studies identify TTR and Klotho as physiological targets of APP that are regulated by soluble APPsβ independent of developmental APP functions. This unexpected APP-mediated signaling pathway may play an important role in maintaining TTR and Klotho levels and their respective functions in Aβ sequestration and aging.
Profile of David J. Mangelsdorf

Raised in Kingman, a sunswept town in the Mojave Desert of northwestern Arizona, Mangelsdorf says his love of nature preceded his love of science. Although much of his work has focused on molecules hidden in cells, his interest in biology began as a passion for marine life in open oceans. Impelled by the breathtaking imagery of French naval explorer Jacques Cousteau’s films of marine life, Mangelsdorf decided to become a marine biologist. “During my sophomore year in high school, I wrote to The Scripps Institution of Oceanography [in San Diego] to explore the option of marine biology as a career. I naively thought I could go there straight from high school, but Scripps did not take undergraduate students,” he says. However, Mangelsdorf learned that one of the best schools in the United States for undergraduate aquatic biology, Northern Arizona University at Flagstaff, was a mere 150 miles from his hometown. In the fall of 1977, he enrolled in the school’s aquatic biology program.
Structural basis of flocculin-mediated social behavior in yeast

In the budding yeast Saccharomyces cerevisiae, self-recognition and the thereby promoted aggregation of thousands of cells into protective flocs is mediated by a family of cell-surface adhesins, the flocculins (Flo). Based on this social behavior FLO genes fulfill the definition of “greenbeard” genes, which direct cooperation toward other carriers of the same gene. The process of flocculation plays an eminent role in the food industry for the production of beer and wine. However, the precise mode of flocculin-mediated surface recognition and the exact structure of cognate ligands have remained elusive. Here, we present structures of the adhesion domain of a flocculin complexed to its cognate ligands derived from yeast high-mannose oligosaccharides at resolutions up to 0.95 Å. Besides a PA14-like architecture, the Flo5A domain reveals a previously undescribed lectin fold that utilizes a unique DcisD calcium-binding motif for carbohydrate binding and that is widely spread among pro- and eukaryotes. Given the high abundance of high-mannose oligosaccharides in yeast cell walls, the Flo5A structure suggests a model for recognition, where social non-self- instead of unsocial self-interactions are favored.
Perceptions of special education academic staff: Who should be employed as special education teachers?

The aim of this study is to identify the perceptions of special education department staff about people employed as special education teachers. In this study, the effects of employment policies upon quality of special education and special education are discussed. In this regard, during the present study, the qualitative data were collected through semi -structured interviews held with academicians (n=24) of special education department in the spring of 2007-2008 academic year on the basis of the interview questions developed by the researcher. Participants pointed out that special education teacher should be the graduates of special education departments, classroom teachers should support special education teachers.
Myelination transition zone astrocytes are constitutively phagocytic and have synuclein dependent reactivity in glaucoma

Optic nerve head (ONH) astrocytes have been proposed to play both protective and deleterious roles in glaucoma. We now show that, within the postlaminar ONH myelination transition zone (MTZ), there are astrocytes that normally express Mac-2 (also known as Lgals3 or galectin-3), a gene typically expressed only in phagocytic cells. Surprisingly, even in healthy mice, MTZ and other ONH astrocytes constitutive internalize large axonal evulsions that contain whole organelles. In mouse glaucoma models, MTZ astrocytes further up-regulate Mac-2 expression. During glaucomatous degeneration, there are dystrophic processes in the retina and optic nerve, including the MTZ, which contain protease resistant γ-synuclein. The increased Mac-2 expression by MTZ astrocytes during glaucoma likely depends on this γ-synuclein, as mice lacking γ-synuclein fail to up-regulate Mac-2 at the MTZ after elevation of intraocular pressure. These results suggest the possibility that a newly discovered normal degradative pathway for axons might contribute to glaucomatous neurodegeneration.
Structural plasticity of a transmembrane peptide allows self-assembly into biologically active nanoparticles

Significant efforts have been devoted to the development of nanoparticular delivering systems targeting tumors. However, clinical application of nanoparticles is hampered by insufficient size homogeneity, difficulties in reproducible synthesis and manufacturing, frequent high uptake in the liver, systemic toxicity of the carriers (particularly for inorganic nanoparticles), and insufficient selectivity for tumor cells. We have found that properly modified synthetic analogs of transmembrane domains of membrane proteins can self-assemble into remarkably uniform spherical nanoparticles with innate biological activity. Self-assembly is driven by a structural transition of the peptide that adopts predominantly a beta-hairpin conformation in aqueous solutions, but folds into an alpha-helix upon spontaneous fusion of the nanoparticles with cell membrane. A 24-amino acid peptide corresponding to the second transmembrane helix of the CXCR4 forms self-assembled particles that inhibit CXCR4 function in vitro and hamper CXCR4-dependent tumor metastasis in vivo. Furthermore, such nanoparticles can encapsulate hydrophobic drugs, thus providing a delivery system with the potential for dual biological activity.
Organic Electrochemical Transistor Array for Recording Transepithelial Ion Transport of Human Airway Epithelial Cells

An organic electrochemical transistor array is integrated with human airway epithelial cells. This integration provides a novel method to couple transepithelial ion transport with electrical current. Activation and inhibition of transepithelial ion transport are readily detected with excellent time resolution. The organic electrochemical transistor array serves as a promising platform for physiological studies and drug testing.