Miracle-dz/UniFAR-FTUs huggingface dataset:
A combined genetic‐morphometric analysis unravels the complex biogeographical history of Polyommatus icarus and Polyommatus celina Common Blue butterflies

Widespread species have the potential to reveal large‐scale biogeographical patterns, as well as responses to environmental changes possibly unique to habitat generalists. This study presents a continental‐scale phylogeographical analysis of Polyommatus icarus, one of the most common Palaearctic butterflies, and the morphologically and ecologically similar Polyommatus celina, a recently discovered cryptic species. By combining data from mitochondrial [cytochrome c oxidase subunit I (COI)] and nuclear [internal transcribed spacer (ITS2)] molecular markers with geometric morphometrics, we document a complex phylogeographical history for the two species. Despite morphological similarities, the genetic divergence between these two species is high (more than 5% at COI) and they are not sister species. For the first time, we show that P. celina occurs not only in North Africa but also in Europe, where it inhabits several west Mediterranean islands, as well as large parts of Iberia, where it occurs in parapatry with P. icarus. The two species appear to completely exclude each other on islands, but we provide morphological and molecular evidence that introgression occurred in the Iberian Peninsula. We discovered strongly diverged lineages that seem to represent relict populations produced by past range expansions and contractions: Crete and Iberian isolates for P. icarus, Balearics–Sardinia and Sicily–Lipari for P. celina. This study shows that a combined genetic‐morphometric approach can shed light on cryptic diversity while providing the necessary resolution to reconstruct a fine‐scale phylogeographical history of species at both spatial and temporal levels.
A biochemical and biophysical model of G-quadruplex DNA recognition by positive coactivator of transcription 4

DNA sequences that are guanine-rich have received considerable attention because of their potential to fold into a secondary, four-stranded DNA structure termed G-quadruplex (G4), which has been implicated in genomic instability and some human diseases. We have previously identified positive coactivator of transcription (PC4), a single-stranded DNA (ssDNA)-binding protein, as a novel G4 interactor. Here, to expand on these previous observations, we biochemically and biophysically characterized the interaction between PC4 and G4DNA. PC4 can bind alternative G4DNA topologies with a low nanomolar Kd value of ∼2 nm, similar to that observed for ssDNA. In consideration of the different structural features between G4DNA and ssDNA, these binding data indicated that PC4 can interact with G4DNA in a manner distinct from ssDNA. The stoichiometry of the PC4-G4 complex was 1:1 for PC4 dimer:G4 substrate. PC4 did not enhance the rate of folding of G4DNA, and formation of the PC4-G4DNA complex did not result in unfolding of the G4DNA structure. We assembled a G4DNA structure flanked by duplex DNA. We find that PC4 can interact with this G4DNA, as well as the complementary C-rich strand. Molecular docking simulations and DNA footprinting experiments suggest a model where a PC4 dimer accommodates the DNA with one monomer on the G4 strand and the second monomer bound to the C-rich strand. Collectively, these data provide a novel mode of PC4 binding to a DNA secondary structure that remains within the framework of the model for binding to ssDNA. Additionally, consideration of the PC4-G4DNA interaction could provide insight into the biological functions of PC4, which remain incompletely understood.
Enhancing Music Features by Knowledge Transfer from User-item Log Data

In this paper, we propose a novel method that exploits music listening log data for general-purpose music feature extraction. Despite the wealth of information available in the log data of user-item interactions, it has been mostly used for collaborative filtering to find similar items or users and was not fully investigated for content-based music applications. We resolve this problem by extending intra-domain knowledge distillation to cross-domain: i.e., by transferring knowledge obtained from the user-item domain to the music content domain. The proposed system first trains the model that estimates log information from the audio contents; then it uses the model to improve other task-specific models. The experiments on various music classification and regression tasks show that the proposed method successfully improves the performances of the task-specific models.
Adenosine and inflammation: CD39 and CD73 are critical mediators in LPS‐induced PMN trafficking into the lungs

Extracellular adenosine has been implicated as anti‐inflammatory signaling molecule during acute lung injury (ALI). The main source of extracellular adenosine stems from a coordinated two‐step enzymatic conversion of precursor nucleotides via the ectoapyrase (CD39) and the ecto‐5'‐nucleotidase (CD73). In the present study, we hypothesized a critical role of CD39 and CD73 in mediating pulmonary neutrophil (PMN) transmigration during lipopolysaccharide (LPS) ‐induced lung injury. Initial studies revealed that pulmonary CD39 and CD73 transcript levels were elevated following LPS exposure in vivo. Moreover, LPS‐induced accumulation of PMN into the lungs was enhanced in cd39−/− or cd73−/− mice, particularly into the interstitial and intra‐alveolar compartment. Such increases in PMN trafficking were accompanied by corresponding changes in alveolar‐capillary leakage. Similarly, inhibition of extracellular nucleotide phosphohydrolysis with the nonspecific ecto‐nucleoside‐triphosphate‐diphosphohydrolases inhibitor POM‐1 confirmed increased pulmonary PMN accumulation in wild‐type, but not in gene‐targeted mice for cd39 or cd73. Finally, treatment with apyrase or nucleotidase was associated with attenuated pulmonary neutrophil accumulation and pulmonary edema during LPS‐induced lung injury. Taken together, these data reveal a previously unrecognized role for CD39 and CD73 in attenuating PMN trafficking into the lungs during LPS‐induced lung injury and suggest treatment with their soluble compounds as a therapeutic strategy. —Reutershan, J., Vollmer, I. , Stark, S. , Wagner, R. , Ngamsri, K. ‐C. , Eltzschig, H. K. Adenosine and inflammation: CD39 and CD73 are critical mediators in LPS‐induced PMN trafficking into the lungs. FASEB J. 23, 473‐482 (2009)
Mice deficient in PKC β and apolipoprotein E display decreased atherosclerosis

Endothelial activation is a central initiating event in atheroma formation. Evidence from our laboratory and others has demonstrated links between activation of early growth response‐1 (Egr‐1) and atherosclerosis and also has demonstrated that activated protein kinase C (PKC) βII is a critical upstream regulator of Egr‐1 in response to vascular stress. We tested the role of PKCβ in regulating key events linked to atherosclerosis and show that the aortas of apoE–/– mice display an age‐dependent increase in PKCβll antigen in membranous fractions vs. C57BL/6 animals with a ~2‐fold increase at age 6 wk and a ~4.5‐fold increase at age 24 wk. Consistent with important roles for PKCβ in atherosclerosis, a significant decrease in atherosclerotic lesion area was evident in PKCβ–/– apoE–/– vs. apoE–/– mice by ~5‐fold, in parallel with significantly reduced vascular transcripts for Egr‐1 and matrix metalloproteinase (MMP)‐2 antigen and activity vs. apoE–/– mice. Significant reduction in atherosclerosis of ~2‐fold was observed in apoE–/– mice fed ruboxistaurin chow (PKCβ inhibitor) vs. vehicle. In primary murine and human aortic endothelial cells, the PKCβ‐JNK mitogen‐activated protein kinase pathway importantly contributes to oxLDL‐mediated induction of MMP2 expression. Blockade of PKCβ may be beneficial in mitigating endothelial perturbation and atherosclerosis. —Harja, E. , Chang, J. S. , Lu, Y. , Leitges, M. , Zou, Y. S. , Schmidt, A. M. , Yan, S. ‐F. Mice deficient in PKC β and apolipoprotein E display decreased atherosclerosis. FASEB J. 23, 1081–1091 (2009)
Genotypic diversity and spatial–temporal distribution of Symbiodinium clones in an abundant reef coral

Genetic data are rapidly advancing our understanding of various biological systems including the ecology and evolution of coral–algal symbioses. The fine‐scale interactions between individual genotypes of host and symbiont remain largely unstudied and constitute a major gap in knowledge. By applying microsatellite markers developed for both host and symbiont, we investigated the intracolony diversity, prevalence and stability of Symbiodinium glynni (type D1) multilocus genotypes in association with dense populations of Pocillopora at two sites in the Gulf of California. The genetic diversity and allelic frequencies in reef populations of S. glynni remained stable over 3 years. Common clone genotypes persisted over this period, and no temporal population subdivision (ΦPT = 0.021 and −0.003) was detected. Collections from circular plots showed no statistical correlation between related Pocillopora individuals and their associations with particular S. glynni genotypes, with no spatial structuring or clonal aggregation across a reef for the symbiont. From permanent linear transects, samples were analysed from multiple locations within a colony and some were resampled approximately 1 year later. Many of these multisampled colonies (approximately 53%) were dominated by a single S. glynni genotype and tended to associate with the same symbiont genotype(s) over time, while colony ramets often possessed unrelated symbiont genotypes. In contrast to the species level, associations between genotypes of Pocillopora and S. glynni are apparently more flexible over space and time. The abundance of sexually recombinant genotypes of S. glynni combined with greater flexibility might provide adaptive mechanisms for these symbioses to evolve rapidly to changes in environmental conditions and allow particular symbiont genotypes to spread through a host population.
The mechanism of ABC transporters: general lessons from structural and functional studies of an antigenic peptide transporter

The shuttling of substrates across a cellular membrane frequently requires a specialized ATP‐ binding cassette (ABC) transporter, which couples the energy of ATP binding and hydrolysis to substrate transport. Due to its importance in immunity, the ABC transporter associated with antigen processing (TAP) has been studied extensively and is an excellent model for other ABC transporters. The TAP protein pumps cytosolic peptides into the endoplasmic reticulum for loading onto class I major histocompatibility complex (MHC) for subsequent immune surveillance. Here, we outline a potential mechanism for the TAP protein with supporting evidence from bacterial transporter structures. The similarities and differences between TAP and other transporters support the notion that ABC transporters in general have adapted around a universal transport mechanism. — Procko, E. , O'Mara, M. L. , Bennett, W. F. D. , Tieleman, D. P., Gaudet, R. The mechanism of ABC transporters: general lessons from structural and functional studies of an antigenic peptide transporter. FASEBJ. 23, 1287–1302 (2009)
Lysosome-mediated degradation of a distinct pool of lipid droplets during hepatic stellate cell activation

Activation of hepatic stellate cells (HSCs) is a critical step in the development of liver fibrosis. During activation, HSCs lose their lipid droplets (LDs) containing triacylglycerols (TAGs), cholesteryl esters, and retinyl esters (REs). We previously provided evidence for the presence of two distinct LD pools, a preexisting and a dynamic LD pool. Here we investigate the mechanisms of neutral lipid metabolism in the preexisting LD pool. To investigate the involvement of lysosomal degradation of neutral lipids, we studied the effect of lalistat, a specific lysosomal acid lipase (LAL/Lipa) inhibitor on LD degradation in HSCs during activation in vitro. The LAL inhibitor increased the levels of TAG, cholesteryl ester, and RE in both rat and mouse HSCs. Lalistat was less potent in inhibiting the degradation of newly synthesized TAG species as compared with a more general lipase inhibitor orlistat. Lalistat also induced the presence of RE-containing LDs in an acidic compartment. However, targeted deletion of the Lipa gene in mice decreased the liver levels of RE, most likely as the result of a gradual disappearance of HSCs in livers of Lipa−/− mice. Lalistat partially inhibited the induction of activation marker α-smooth muscle actin (α-SMA) in rat and mouse HSCs. Our data suggest that LAL/Lipa is involved in the degradation of a specific preexisting pool of LDs and that inhibition of this pathway attenuates HSC activation.
The S1 helix critically regulates the finely tuned gating of Kv11.1 channels

Congenital mutations in the cardiac Kv11.1 channel can cause long QT syndrome type 2 (LQTS2), a heart rhythm disorder associated with sudden cardiac death. Mutations act either by reducing protein expression at the membrane and/or by perturbing the intricate gating properties of Kv11.1 channels. A number of clinical LQTS2-associated mutations have been reported in the first transmembrane segment (S1) of Kv11.1 channels, but the role of this region of the channel is largely unexplored. In part, this is due to problems defining the extent of the S1 helix, as a consequence of its low sequence homology with other Kv family members. Here, we used NMR spectroscopy and electrophysiological characterization to show that the S1 of Kv11.1 channels extends seven helical turns, from Pro-405 to Phe-431, and is flanked by unstructured loops. Functional analysis suggests that pre-S1 loop residues His-402 and Tyr-403 play an important role in regulating the kinetics and voltage dependence of channel activation and deactivation. Multiple residues within the S1 helix also play an important role in fine-tuning the voltage dependence of activation, regulating slow deactivation, and modulating C-type inactivation of Kv11.1 channels. Analyses of LQTS2-associated mutations in the pre-S1 loop or S1 helix of Kv11.1 channels demonstrate perturbations to both protein expression and most gating transitions. Thus, S1 region mutations would reduce both the action potential repolarizing current passed by Kv11.1 channels in cardiac myocytes, as well as the current passed in response to premature depolarizations that normally helps protect against the formation of ectopic beats.
Insights into the mechanical properties of epithelial cells: the effects of shear stress on the assembly and remodeling of keratin intermediate filaments

The effects of shear stress on the keratin intermediate filament (KIF) cytoskeleton of cultured human alveolar epithelial (A549) cells have been investigated. Under normal culture conditions, immunofluorescence revealed a delicate network of fine tonofibrils containing KIFs, together with many nonfilamentous, keratin‐containing “particles,” mostly containing either keratin 8 (K8) or 18 (K18), but not both. Triton X‐100 extracted ~10% of the cellular keratin, and this was accompanied by a loss of the particles but not the KIFs. Shear stress dramatically reduced the soluble keratin component and transformed the fine bundles of KIFs into thicker, “wavy” tonofibrils. Both effects were accompanied by the disappearance of most keratin particles and by increased phosphorylation of K8 and K18 on serine residues 73 and 33, respectively. The particles that remained after shearing were phosphorylated and were closely associated with KIFs. We suggest that keratin particles constitute a reservoir of protein that can be recruited into KIFs under flow, creating a more robust cytoskeleton able to withstand shear forces more effec‐tively. —Flitney, E. W. , Kuczmarski, E. R. , Adam, S. A. , Goldman, R. D. Insights into the mechanical properties of epithelial cells: the effects of shear stress on the assembly and remodeling of keratin intermediate filaments. FASEB J. 23, 2110–2119 (2009)
Proteomics in evolutionary ecology: linking the genotype with the phenotype

The study of the proteome (proteomics), which includes the dynamics of protein expression, regulation, interactions and its function, has played a less prominent role in evolutionary and ecological investigations in comparison with the study of the genome and transcriptome. There are, however, a number of arguments suggesting that this situation should change. First, the proteome is closer to the phenotype than the genome or the transcriptome, and as such may be more directly responsive to natural selection, and thus closely linked to adaptation. Second, there is evidence of a low correlation between protein and transcript expression levels across genes in many different organisms. Finally, there have been some recent important technological improvements in proteomics methods that make them feasible, practical and useful to address a wide range of evolutionary questions even in nonmodel organisms. The different proteomic methods, their limitations and problems when interpreting empirical data are described and discussed. In addition, the proteomic literature pertaining to evolutionary ecology is reviewed with examples, and potential applications of proteomics in a variety of evolutionary contexts are outlined. New proteomic research trends such as the study of posttranslational modifications and protein–protein interactions, as well as the combined use of the different ‐omics approaches, are discussed in relation to the development of a more functional and integrated perspective, needed for achieving a more comprehensive knowledge of evolutionary change.
skNAC (skeletal Naca), a muscle‐specific isoform of Naca (nascent polypeptide‐associated complex alpha), is required for myofibril organization

Myofibrillogenesis, the precise assembly of sarcomeric proteins into the highly organized sarcomeres, is essential for muscle cell differentiation and function. Myofibrillogenesis requires proper folding and assembly of newly synthesized sarcomeric proteins. sknac (skeletal naca) is an alternatively spliced isoform of naca, which encodes the nascent polypeptide‐associated complex alpha polypeptide that binds to newly synthesized polypeptides emerging from the ribosome. sknac is specifically expressed in skeletal and cardiac muscles. However, little is known about the function of skNAC in muscle development in vivo. To determine skNAC function, we have isolated and characterized the sknac gene from zebrafish. Zebrafish sknac cDNA differs from naca by containing an extra large exon that encodes 815 aa. Knockdown of sknac expression by antisense oligos resulted in zebrafish embryos with skeletal muscle defects. The sknac‐knockdown embryos showed a paralyzed phenotype with little muscle contraction. In contrast, injection of a control oligo had no effect. Immunostaining and histological analyses revealed that sknac‐knockdown embryos contained disorganized thick and thin filaments. Western blot analysis revealed that myosin protein levels were significantly reduced. Collectively, these results demonstrate that skNAC plays a vital role in myofibril assembly and function during muscle cell differentiation. —Li, H. , Randall, W.R. , Du, S. ‐J. SkNAC (skeletal Naca), a muscle‐specific isoform of Naca (nascent polypeptide‐associated complex alpha), is required for myofibril organization in zebrafish embryo. FASEB J. 23, 1988–2000 (2009)
Pathogenic Acinetobacter species have a functional type I secretion system and contact-dependent inhibition systems

Pathogenic Acinetobacter species, including Acinetobacter baumannii and Acinetobacter nosocomialis, are opportunistic human pathogens of increasing relevance worldwide. Although their mechanisms of drug resistance are well studied, the virulence factors that govern Acinetobacter pathogenesis are incompletely characterized. Here we define the complete secretome of A. nosocomialis strain M2 in minimal medium and demonstrate that pathogenic Acinetobacter species produce both a functional type I secretion system (T1SS) and a contact-dependent inhibition (CDI) system. Using bioinformatics, quantitative proteomics, and mutational analyses, we show that Acinetobacter uses its T1SS for exporting two putative T1SS effectors, an Repeats-in-Toxin (RTX)-serralysin-like toxin, and the biofilm-associated protein (Bap). Moreover, we found that mutation of any component of the T1SS system abrogated type VI secretion activity under nutrient-limited conditions, indicating a previously unrecognized cross-talk between these two systems. We also demonstrate that the Acinetobacter T1SS is required for biofilm formation. Last, we show that both A. nosocomialis and A. baumannii produce functioning CDI systems that mediate growth inhibition of sister cells lacking the cognate immunity protein. The Acinetobacter CDI systems are widely distributed across pathogenic Acinetobacter species, with many A. baumannii isolates harboring two distinct CDI systems. Collectively, these data demonstrate the power of differential, quantitative proteomics approaches to study secreted proteins, define the role of previously uncharacterized protein export systems, and observe cross-talk between secretion systems in the pathobiology of medically relevant Acinetobacter species.
Protease-activated receptor-4 and purinergic receptor P2Y12 dimerize, co-internalize, and activate Akt signaling via endosomal recruitment of β-arrestin

Vascular inflammation and thrombosis require the concerted actions of several different agonists, many of which act on G protein-coupled receptors (GPCRs). GPCR dimerization is a well-established phenomenon that can alter protomer function. In platelets and other cell types, protease-activated receptor-4 (PAR4) has been shown to dimerize with the purinergic receptor P2Y12 to coordinate β-arrestin–mediated Akt signaling, an important mediator of integrin activation. However, the mechanism by which the PAR4-P2Y12 dimer controls β-arrestin–dependent Akt signaling is not known. We now report that PAR4 and P2Y12 heterodimer internalization is required for β-arrestin recruitment to endosomes and Akt signaling. Using bioluminescence resonance energy transfer, immunofluorescence microscopy, and co-immunoprecipitation in cells expressing receptors exogenously and endogenously, we demonstrate that PAR4 and P2Y12 specifically interact and form dimers expressed at the cell surface. We also found that activation of PAR4 but not of P2Y12 drives internalization of the PAR4-P2Y12 heterodimer. Remarkably, activated PAR4 internalization was required for recruitment of β-arrestin to endocytic vesicles, which was dependent on co-expression of P2Y12. Interestingly, stimulation of the PAR4-P2Y12 heterodimer promotes β-arrestin and Akt co-localization to intracellular vesicles. Moreover, activated PAR4-P2Y12 internalization is required for sustained Akt activation. Thus, internalization of the PAR4-P2Y12 heterodimer is necessary for β-arrestin recruitment to endosomes and Akt signaling and lays the foundation for examining whether blockade of PAR4 internalization reduces integrin and platelet activation.