Miracle-dz/UniFAR-FTUs huggingface dataset:
A Two-component NADPH Oxidase (NOX)-like System in Bacteria Is Involved in the Electron Transfer Chain to the Methionine Sulfoxide Reductase MsrP*

MsrPQ is a newly identified methionine sulfoxide reductase system found in bacteria, which appears to be specifically involved in the repair of periplasmic proteins oxidized by hypochlorous acid. It involves two proteins: a periplasmic one, MsrP, previously named YedY, carrying out the Msr activity, and MsrQ, an integral b-type heme membrane-spanning protein, which acts as the specific electron donor to MsrP. MsrQ, previously named YedZ, was mainly characterized by bioinformatics as a member of the FRD superfamily of heme-containing membrane proteins, which include the NADPH oxidase proteins (NOX/DUOX). Here we report a detailed biochemical characterization of the MsrQ protein from Escherichia coli. We optimized conditions for the overexpression and membrane solubilization of an MsrQ-GFP fusion and set up a purification scheme allowing the production of pure MsrQ. Combining UV-visible spectroscopy, heme quantification, and site-directed mutagenesis of histidine residues, we demonstrated that MsrQ is able to bind two b-type hemes through the histidine residues conserved between the MsrQ and NOX protein families. In addition, we identify the E. coli flavin reductase Fre, which is related to the dehydrogenase domain of eukaryotic NOX enzymes, as an efficient cytosolic electron donor to the MsrQ heme moieties. Cross-linking experiments as well as surface Plasmon resonance showed that Fre interacts with MsrQ to form a specific complex. Taken together, these data support the identification of the first prokaryotic two-component protein system related to the eukaryotic NOX family and involved in the reduction of periplasmic oxidized proteins.
Locating Transparent Objects to Millimetre Accuracy

Transparent surfaces, such as glass, transmit most of the visible light that falls on them, making accurate pose estimation challenging. We propose a method to locate glass objects to millimetre accuracy using a simple Laser Range Finder (LRF) attached to the robot end-effector. The method, derived from a physical understanding of laser-glass interactions, consists of (i) sampling points on the glass border by looking at the glass surface from an angle of approximately 45 degrees, and (ii) performing Iterative Closest Point registration on the sampled points. We verify experimentally that the proposed method can locate a transparent, non-planar, side car glass to millimetre accuracy.
A new method for estimating effective population sizes from a single sample of multilocus genotypes

Equations for the effective size (Ne) of a population were derived in terms of the frequencies of a pair of offspring taken at random from the population being sibs sharing the same one or two parents. Based on these equations, a novel method (called sibship assignment method) was proposed to infer Ne from the sibship frequencies estimated from a sibship assignment analysis, using the multilocus genotypes of a sample of offspring taken at random from a single cohort in a population. Comparative analyses of extensive simulated data and some empirical data clearly demonstrated that the sibship assignment method is much more accurate [measured by the root mean squared error, RMSE, of 1/(2Ne)] than other methods such as the heterozygote excess method, the linkage disequilibrium method, and the temporal method. The RMSE of 1/(2Ne) from the sibship assignment method is typically a small fraction of that from other methods. The new method is also more general and flexible than other methods. It can be applied to populations with nonoverlapping generations of both diploid and haplodiploid species under random or nonrandom mating, using either codominant or dominant markers. It can also be applied to the estimation of Ne for a subpopulation with immigration. With some modification, it could be applied to monoecious diploid populations with self‐fertilization, and to populations with overlapping generations.
Structural and bioinformatic analysis of the Roman snail Cd‐Metallothionein gene uncovers molecular adaptation towards plasticity in coping with multifarious environmental stress

Metallothioneins (MTs) are a family of multifunctional proteins involved, among others, in stress response. The Cadmium (Cd)‐MT gene of the Roman snail (Helix pomatia), for example, encodes for a protein induced upon cadmium exposure. While our previous studies have demonstrated that the expressed Cd‐MT isoform of Roman snails assists detoxification of cadmium, the present work focuses on the potential plasticity of this gene in response to a variety of environmental stressors playing a crucial role in the specific ecological niche of H. pomatia. Our hypothesis is based on a bioinformatic approach involving gene sequencing, structural and in silico analysis of transcription factor binding sites (TFBs), and a comparison of these features with other MT genes. Our results show that the Roman snail's Cd‐MT gene not only is the largest known MT gene, but also contains — apart from the regulatory promoter region — several intronic repeat cassettes of putative TFBs suggested to be involved in environmental stress response, immune competence, and regulation of gene expression. Moreover, intronic scaffold/matrix attachment regions (S/MARs) and stress‐induced duplex destabilization sites confer a high potential for epigenetic gene regulation. This suggested regulatory plasticity is also supported by physiological data showing that Cd‐MT in Roman snails can be induced differentially not only after cadmium exposure, but also in response to nonmetallic environmental stressors. It is concluded that structural analysis combined with bioinformatic screening may constitute valuable tools for predicting the potential for plasticity and niche‐specific adaptation of stress‐responsive genes in populations living under rapidly changing environmental conditions.
Patchy population structure in a short‐distance migrant: evidence from genetic and demographic data

Species often occur in subdivided populations as a consequence of spatial heterogeneity of the habitat. To describe the spatial organization of subpopulations, existing theory proposes three main population models: patchy population, metapopulation and isolated populations. These models differ in their predicted levels of connectivity among subpopulations, and in the risk that a subpopulation will go extinct. However, spatially discrete subpopulations are commonly considered to be organized as metapopulations, even though explicit tests of metapopulation assumptions are rare. Here, we test predictions of the three models on the basis of demographic and genetic data, a combined approach so far surprisingly little used in mobile organisms. From 2002 to 2005, we studied nine subpopulations of the wetland‐restricted reed bunting (Emberiza schoeniclus) in the southeastern part of the Canton Zurich (Switzerland), from which local declines of this species have been reported. Here, wetlands are as small as 2.7 ha and separated through intensively used agricultural landscapes. Demographic data consisted of dispersal of colour‐banded individuals among subpopulations, immigration rates and extinction‐/recolonization dynamics. Genetic data were based on the distribution of genetic variability and gene flow among subpopulations derived from the analysis of nine microsatellite loci. Both demographic and genetic data revealed that the patchy population model best described the spatial organization of reed bunting subpopulations. High levels of dispersal among subpopulations, high immigration into the patchy population, and genetic admixture suggested little risk of extinction of both subpopulations and the entire patchy population. This study exemplifies the idea that spatially discrete subpopulations may be organized in ways other than a metapopulation, and hence has implications for the conservation of subpopulations and species.
Variable patterns of introgression in two sculpin hybrid zones suggest that genomic isolation differs among populations

Theory predicts that reproductive isolation may be due to intrinsic genetic incompatibilities or extrinsic ecological factors. Therefore, an understanding of the genetic basis of isolation may require analyses of evolutionary processes in situ to include environmental factors. Here we study genetic isolation between populations of sculpins (Cottus) at 168 microsatellites. Genomic clines were fit using 480 individuals sampled across independent natural hybrid zones that have formed between one invading species and two separate populations of a resident species. Our analysis tests for deviations from neutral patterns of introgression at individual loci based on expectations given genome‐wide admixture. Roughly 51% of the loci analysed displayed significant deviations. An overall deficit of interspecific heterozygotes in 26% and 21% of the loci suggests that widespread underdominance drives genomic isolation. At the same time, selection promotes introgression of almost 30% of the markers, which implies that hybridization may increase the fitness of admixed individuals. Cases of overdominance or epistatic interactions were relatively rare. Despite the similarity of the two hybrid zones in their overall genomic composition, patterns observed at individual loci show little correlation between zones and many fit different genotypic models of fitness. At this point, it remains difficult to determine whether these results are due to differences in external selection pressures or cryptic genetic differentiation of distinct parental populations. In the future, data from mapped genetic markers and on variation of ecological factors will provide additional insights into the contribution of these factors to variation in the evolutionary consequences of hybridization.
Genetic, morphological, and feather isotope variation of migratory willow warblers show gradual divergence in a ring

The circular distribution of the willow warbler Phylloscopus trochilus around the Baltic Sea shares many features with the classic examples of ring species; however, the system is much younger. It has previously been shown that a secondary contact zone is located in central Scandinavia, where there are narrow clines for several morphological traits coincident with a migratory divide. Here we analyse multiple traits and genes from > 1700 males captured on breeding territories at 77 sites spread around the Baltic Sea to test the following hypothesis. If the secondary contact zone in Scandinavia is a result of divergence in two allopatric refuge populations during the last glaciation, we expect to find a similar secondary contact zone somewhere else around the circular distribution. Our results show that the trait clines were wider and displaced from each other along the eastern side of the Baltic Sea. Analyses of 12 microsatellite loci confirmed that the genome is very similar between the terminal forms (FST = 0). Two AFLP‐derived markers filtered out from a genomic scan instead appear to be maintained by selection. These markers exhibited steep clines at the secondary contact zone in Scandinavia, but as for the phenotypic traits, had vastly different cline centres east of the Baltic Sea. The trait clines along the ring distribution outside the Scandinavian secondary contact zone thus seem to have been shaped by independent action of selection or drift during the process of postglacial colonization.
The Basophil-specific Protease mMCP-8 Provokes an Inflammatory Response in the Skin with Microvascular Hyperpermeability and Leukocyte Infiltration*

Basophils have often been erroneously considered to be minor relatives or blood-circulating precursors of tissue-resident mast cells because of some phenotypic similarity between them, including basophilic secretory granules in the cytoplasm. However, recent studies revealed that the repertoire of serine proteases stored in secretory granules is distinct in them. Particularly, mouse mast cell protease 8 (mMCP-8) is specifically expressed by basophils but not mast cells despite its name. Therefore, mMCP-8 is commonly used as a basophil-specific marker, but its functional property remains uncertain. Here we prepared recombinant mMCP-8 and examined its activity in vitro and in vivo. Purified recombinant mMCP-8 showed heat-sensitive proteolytic activity when α-tubulin was used as a substrate. One intradermal shot of mMCP-8, not heat-inactivated, induced cutaneous swelling with increased microvascular permeability in a cyclooxygenase-dependent manner. Moreover, repeated intradermal injection of mMCP-8 promoted skin infiltration of leukocytes, predominantly neutrophils and, to a lesser extent, monocytes and eosinophils, in conjunction with up-regulation of chemokine expression in the skin lesion. These results suggest that mMCP-8 is an important effector molecule in basophil-elicited inflammation, providing novel insights into how basophils exert a crucial and non-redundant role, distinct from that played by mast cells, in immune responses.
Steroidogenic Factor 1 Differentially Regulates Fetal and Adult Leydig Cell Development in Male Mice1

ABSTRACT The nuclear receptor steroidogenic factor 1 (SF-1, AD4BP, NR5A1) is a key regulator of the endocrine axes and is essential for adrenal and gonad development. Partial rescue of Nr5a1−/− mice with an SF-1-expressing transgene caused a hypomorphic phenotype that revealed its roles in Leydig cell development. In contrast to controls, all male rescue mice (Nr5a1−/−;tg+/0) showed varying signs of androgen deficiency, including spermatogenic arrest, cryptorchidism, and poor virilization. Expression of various Leydig cell markers measured by immunohistochemistry, Western blot analysis, and RT-PCR indicated fetal and adult Leydig cell development were differentially impaired. Whereas fetal Leydig cell development was delayed in Nr5a1−/−;tg+/0 embryos, it recovered to control levels by birth. In contrast, Sult1e1, Vcam1, and Hsd3b6 transcript levels in adult rescue testes indicated complete blockage in adult Leydig cell development. In addition, between Postnatal Days 8 and 12, peritubular cells expressing PTCH1, SF-1, and CYP11A1 were observed in control testes but not in rescue testes, indicating SF-1 is needed for either survival or differentiation of adult Leydig cell progenitors. Cultured prepubertal rat peritubular cells also expressed SF-1 and PTCH1, but Cyp11a1 was expressed only after treatment with cAMP and retinoic acid. Together, data show SF-1 is needed for proper development of fetal and adult Leydig cells but with distinct primary functions; in fetal Leydig cells, it regulates differentiation, whereas in adult Leydig cells it regulates progenitor cell formation and/or survival.
Generative Graph Convolutional Network for Growing Graphs

Modeling generative process of growing graphs has wide applications in social networks and recommendation systems, where cold start problem leads to new nodes isolated from existing graph. Despite the emerging literature in learning graph representation and graph generation, most of them can not handle isolated new nodes without nontrivial modifications. The challenge arises due to the fact that learning to generate representations for nodes in observed graph relies heavily on topological features, whereas for new nodes only node attributes are available. Here we propose a unified generative graph convolutional network that learns node representations for all nodes adaptively in a generative model framework, by sampling graph generation sequences constructed from observed graph data. We optimize over a variational lower bound that consists of a graph reconstruction term and an adaptive Kullback-Leibler divergence regularization term. We demonstrate the superior performance of our approach on several benchmark citation network datasets.
Ethanol Extracts from Thai Plants have Anti-Plasmodium and Anti-Toxoplasma Activities In Vitro

The ethanol extracts from seven Thai plants, Kaempferia parviflora, Stemona tuberosa Lour. , Ananas comosus, Punica granatum, Musa sapientum L. , Pseuderanthemum palatiferum and Annona muricata L. , which are traditionally used in Thailand to support human health, were evaluated for their anti-Plasmodium and anti-Toxoplasma activities, and for their cytotoxicities against human foreskin fibroblasts in vitro. The K. parviflora, P. palatiferum and A. muricata extracts were active against P. falciparum (3D7) with selectivity index (SI) values > 10, while their half maximal inhibitory concentrations (IC50) were 28.7 µg/ml, 78.8 µg/ml and 46.1 µg/ml, respectively. Extracts from K. parviflora and M. sapientum (ripe fruit peel) inhibited T. gondii (RH) growth with IC50 values of 53.5 µg/ml and 90.4 µg/ml, respectively. The SI values of the extracts from K. parviflora and M. sapientum (ripe fruit peel) were 9.0 and 10.8, respectively. Our data show that some of the aforementioned ethanol extracts are potential sources of new drugs to treat Plasmodium and Toxoplasma infections.
How does farmer connectivity influence livestock genetic structure? A case‐study in a Vietnamese goat population

Assessing how genes flow across populations is a key component of conservation genetics. Gene flow in a natural population depends on ecological traits and the local environment, whereas for a livestock population, gene flow is driven by human activities. Spatial organization, relationships between farmers and their husbandry practices will define the farmer’s network and so determine farmer connectivity. It is thus assumed that farmer connectivity will affect the genetic structure of their livestock. To test this hypothesis, goats reared by four different ethnic groups in a Vietnamese province were genotyped using 16 microsatellites. A Bayesian approach and spatial multivariate analysis (spatial principal component analysis, sPCA) were used to identify subpopulations and spatial organization. Ethnic group frequencies, husbandry practices and altitude were used to create cost maps that were implemented in a least‐cost path approach. Genetic diversity in the Vietnamese goat population was low (0.508) compared to other local Asian breeds. Using a Bayesian approach, three clusters were identified. sPCA confirmed these three clusters and also that the genetic structure showed a significant spatial pattern. The least‐cost path analysis showed that genetic differentiation was significantly correlated (0.131–0.207) to ethnic frequencies and husbandry practices. In brief, the spatial pattern observed in the goat population was the result of complex gene flow governed by the spatial distribution of ethnic groups, ethnicity and husbandry practices. In this study, we clearly linked the livestock genetic pattern to farmer connectivity and showed the importance of taking into account spatial information in genetic studies.
Cross-talk between the glucocorticoid receptor and MyoD family inhibitor domain-containing protein provides a new mechanism for generating tissue-specific responses to glucocorticoids

Glucocorticoids are primary stress hormones that regulate many physiological processes, and synthetic derivatives of these molecules are widely used in the clinic. The molecular factors that govern tissue specificity of glucocorticoids, however, are poorly understood. The actions of glucocorticoids are mediated by the glucocorticoid receptor (GR). To discover new proteins that interact with GR and modulate its function, we performed a yeast two-hybrid assay. The MyoD family inhibitor domain-containing protein (MDFIC) was identified as a binding partner for GR. MDFIC associated with GR in the cytoplasm of cells, and treatment with glucocorticoids resulted in the dissociation of the GR-MDFIC complex. To investigate the function of the GR-MDFIC interaction, we performed a genome-wide microarray in intact and MDFIC-deficient A549 cells that were treated with glucocorticoids. A large cohort of genes was differentially regulated by GR depending on the presence or absence of MDFIC. These gene changes were strongly associated with inflammation, and glucocorticoid regulation of the inflammatory response was altered in MDFIC-deficient cells. At a molecular level, the interaction of MDFIC with GR altered the phosphorylation status of the receptor. We demonstrate in COS-1 cells that changes in receptor phosphorylation underlie the ability of MDFIC to regulate the transcriptional activity of GR. Finally, we show that GR directly represses the MDFIC gene, revealing a negative feedback loop by which glucocorticoids limit MDFIC activity. These findings identify a new binding partner for cytoplasmic GR that modulates the receptor transcriptome and contributes to the tissue-specific actions of glucocorticoids.
The Activating C-type Lectin-like Receptor NKp65 Signals through a Hemi-immunoreceptor Tyrosine-based Activation Motif (hemITAM) and Spleen Tyrosine Kinase (Syk)*

NKp65 is an activating human C-type lectin-like receptor (CTLR) triggering cellular cytotoxicity and cytokine secretion upon high-affinity interaction with the cognate CTLR keratinocyte-associated C-type lectin (KACL) selectively expressed by human keratinocytes. Previously, we demonstrated that NKp65-mediated cellular cytotoxicity depends on tyrosine 7, located in a cytoplasmic sequence motif of NKp65 resembling a hemi-immunoreceptor tyrosine-based activation motif (hemITAM). HemITAMs have been reported for a few activating myeloid-specific CTLRs, including Dectin-1 and CLEC-2, and consist of a single tyrosine signaling unit preceded by a triacidic motif. Upon receptor engagement, the hemITAM undergoes phosphotyrosinylation and specifically recruits spleen tyrosine kinase (Syk), initiating cellular activation. In this study, we addressed the functionality of the putative hemITAM of NKp65. We show that NKp65 forms homodimers and is phosphorylated at the hemITAM-embedded tyrosine 7 upon engagement by antibodies or KACL homodimers. HemITAM phosphotyrosinylation initiates a signaling pathway involving and depending on Syk, leading to cellular activation and natural killer (NK) cell degranulation. However, although NKp65 utilizes Syk for NK cell activation, a physical association of Syk with the NKp65 hemITAM could not be detected, unlike shown previously for the hemITAM of myeloid CTLR. Failure of NKp65 to recruit Syk is not due to an alteration of the triacidic motif, which rather affects the efficiency of hemITAM phosphotyrosinylation. In summary, NKp65 utilizes a hemITAM-like motif for cellular activation that requires Syk, although Syk appears not to be recruited to NKp65.
Deep phylogeographic divisions and long‐term persistence of forest invertebrates (Hexapoda: Collembola) in the North‐Western Mediterranean basin

The North‐Western Mediterranean basin is well known for its high number of relictual endemic taxa, and has been indicated as one of the world’s major biodiversity hotspots at the species level. A possible contributing factor may be long‐term persistence of populations and their prolonged stability. This study was designed to investigate the phylogeographic structure of three common species of the genus Lepidocyrtus (Hexapoda: Collembola), soil‐dwelling arthropods characterized by limited dispersal capabilities and generally associated with forest habitats. We observed a remarkable geographic structure, with numerous deeply divergent genetic lineages occupying islands as well as mainland sites with no apparent gene flow among most sites, even across distances of only tens of kilometres. The reconstructed time frame for the evolution of these lineages suggests divergence between 5 and 15 Ma. This indicates a remarkably ancient origin and long‐term persistence of individual lineages over a fine geographic scale despite the occurrence of abrupt sea level and climatic fluctuations in the area. This further suggests that currently recognized morphological species might be a serious underestimation of the true springtail biodiversity within this region.