Genome surveyor 2.0: cis-regulatory analysis in Drosophila

Genome Surveyor 2.0 is a web-based tool for discovery and analysis of cis-regulatory elements in Drosophila, built on top of the GBrowse genome browser for convenient visualization. Genome Surveyor was developed as a tool for predicting transcription factor (TF) binding targets and cis-regulatory modules (CRMs/enhancers), based on motifs representing experimentally determined DNA binding specificities. Since its first publication, we have added substantial new functionality (e.g. phylogenetic averaging of motif scores from multiple species, and a novel CRM discovery technique), increased the number of supported motifs about 4-fold (from approximately 100 to approximately 400), added provisions for evolutionary comparison across many more Drosophila species (from 2 to 12), and improved the user-interface. The server is free and open to all users, and there is no login requirement. Address: http://veda.cs.uiuc.edu/gs

Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism

Characterization of cell type specific regulatory networks and elements is a major challenge in genomics, and emerging strategies frequently employ high-throughput genome-wide assays of transcription factor (TF) to DNA binding, histone modifications or chromatin state. However, these experiments remain too difficult/expensive for many laboratories to apply comprehensively to their system of interest. Here, we explore the potential of elucidating regulatory systems in varied cell types using computational techniques that rely on only data of gene expression, low-resolution chromatin accessibility, and TF-DNA binding specificities (\u27motifs\u27). We show that static computational motif scans overlaid with chromatin accessibility data reasonably approximate experimentally measured TF-DNA binding. We demonstrate that predicted binding profiles and expression patterns of hundreds of TFs are sufficient to identify major regulators of approximately 200 spatiotemporal expression domains in the Drosophila embryo. We are then able to learn reliable statistical models of enhancer activity for over 70 expression domains and apply those models to annotate domain specific enhancers genome-wide. Throughout this work, we apply our motif and accessibility based approach to comprehensively characterize the regulatory network of fruitfly embryonic development and show that the accuracy of our computational method compares favorably to approaches that rely on data from many experimental assays. Acids Research

Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development

Regulation of eukaryotic gene transcription is often combinatorial in nature, with multiple transcription factors (TFs) regulating common target genes, often through direct or indirect mutual interactions. Many individual examples of cooperative binding by directly interacting TFs have been identified, but it remains unclear how pervasive this mechanism is during animal development. Cooperative TF binding should be manifest in genomic sequences as biased arrangements of TF-binding sites. Here, we explore the extent and diversity of such arrangements related to gene regulation during Drosophila embryogenesis. We used the DNA-binding specificities of 322 TFs along with chromatin accessibility information to identify enriched spacing and orientation patterns of TF-binding site pairs. We developed a new statistical approach for this task, specifically designed to accurately assess inter-site spacing biases while accounting for the phenomenon of homotypic site clustering commonly observed in developmental regulatory regions. We observed a large number of short-range distance preferences between TF-binding site pairs, including examples where the preference depends on the relative orientation of the binding sites. To test whether these binding site patterns reflect physical interactions between the corresponding TFs, we analyzed 27 TF pairs whose binding sites exhibited short distance preferences. In vitro protein-protein binding experiments revealed that \u3e65% of these TF pairs can directly interact with each other. For five pairs, we further demonstrate that they bind cooperatively to DNA if both sites are present with the preferred spacing. This study demonstrates how DNA-binding motifs can be used to produce a comprehensive map of sequence signatures for different mechanisms of combinatorial TF action

In vitro effect of honey on Candida albicans and lactobacillus

زمینه و هدف: یکی از شایع ترین واژینیت ها در زنان واژینیت های کاندیدایی است که عامل آن قارچ کاندیدا آلبیکنس می باشد. لاکتوباسیلوس از شایع ترین فلورهای طبیعی واژن می باشد که در حفظ شرایط میکروبیولوژی واژن اهمیت زیادی دارد. این مطالعه با هدف بررسی آزمایشگاهی تاثیر عسل بر کاندیدا آلبیکنس و لاکتوباسیلوس انسانی انجام شده است. روش بررسی: در این مطالعه تجربی آزمایشگاهی غلظت های مختلف (وزنی حجمی) بین 20 تا 95 درصد عسل تهیه شد. پس از کشت کاندیدا در محیط کشت RPMI 1640 و عسل و لاکتوباسیلوس در محیط کشت تریپتی کیس سوی براث (TBS) و عسل و انکوباسیون، میزان رشد این میکروارگانسیم ها در ساعات مختلف مورد برسی قرار گرفت. یافته ها: ازغلظت های مورد بررسی، غلظت80 عسل به میزان زیادی از رشد کاندیدا جلوگیری نمود که بیشترین تاثیر مهار کنندگی عسل بر کاندیدا را نشان داد. در محیط های حاوی عسل با غلظت های کمتر و بیشتر از 80 میزان رشد کاندیدا متوسط یا شدید بود. در محیط کشت شاهد، قارچ به طور کامل رشد نمود. هیچکدام از غلظت های عسل نتوانست رشد لاکتوباسیلوس را مهار نماید. نتیجه گیری: با توجه به نتایج بدست آمده عسل می تواند به طور قابل توجهی از رشد کاندیدا جلوگیری کند بدون اینکه تاثیری بر روی لاکتوباسیلوس داشته باشد. با توجه به اینکه لاکتوباسیلوس یک فلور طبیعی واژن است، این مسئله حائز اهمیت است که عسل بدون تغییر فلور طبیعی واژن می تواند رشد کاندیدا را مهار نماید

CDK8 Fine-Tunes IL-6 Transcriptional Activities by Limiting STAT3 Resident Time at the Gene Loci

International audienceCytokines are highly pleiotropic ligands that regulate the immune response. Here, using interleukin-6 (IL-6) as a model system, we perform detailed phosphoproteomic and transcriptomic studies in human CD4+ T helper 1 (Th-1) cells to address the molecular bases defining cytokine functional pleiotropy. We identify CDK8 as a negative regulator of STAT3 transcriptional activities, which interacts with STAT3 upon IL-6 stimulation. Inhibition of CDK8 activity, using specific small molecule inhibitors, reduces the IL-6-induced phosphoproteome by 23% in Th-1 cells, including STAT3 S727 phosphorylation. STAT3 binding to target DNA sites in the genome is increased upon CDK8 inhibition, which results in a concomitant increase in STAT3-mediated transcriptional activity. Importantly, inhibition of CDK8 activity under Th-17 polarizing conditions results in an enhancement of Th-17 differentiation. Our results support a model where CDK8 regulates STAT3 transcriptional processivity by modulation of its gene loci resident time, critically contributing to diversification of IL-6 responses

Soft X-ray phase nano-microscopy of micrometre-thick magnets

Imaging of nanoscale magnetic textures within extended material systems is of critical importance both to fundamental research and technological applications. Whilst high resolution magnetic imaging of thin nanoscale samples is well-established with electron and soft X-ray microscopy, the extension to micrometer-thick systems with hard X-rays currently limits high resolution imaging to rare-earth magnets. Here we overcome this limitation by establishing soft X-ray magnetic imaging of micrometer-thick systems using the pre-edge phase X-ray Magnetic Circular Dichroism signal, thus making possible the study of a wide range of magnetic materials. By performing dichroic spectro-ptychography, we demonstrate high spatial resolution imaging of magnetic samples up to 1.7 {\mu}m thick, an order of magnitude higher than conventionally possible with absorption-based techniques. This new regime of magnetic imaging makes possible the study of extended non rare-earth systems that have until now been inaccessible, from magnetic textures for future spintronic applications to non-rare-earth permanent magnets

Prediction of Breeding Values for Dairy Cattle Using Artificial Neural Networks and Neuro-Fuzzy Systems

Developing machine learning and soft computing techniques has provided many opportunities for researchers to establish new analytical methods in different areas of science. The objective of this study is to investigate the potential of two types of intelligent learning methods, artificial neural networks and neuro-fuzzy systems, in order to estimate breeding values (EBV) of Iranian dairy cattle. Initially, the breeding values of lactating Holstein cows for milk and fat yield were estimated using conventional best linear unbiased prediction (BLUP) with an animal model. Once that was established, a multilayer perceptron was used to build ANN to predict breeding values from the performance data of selection candidates. Subsequently, fuzzy logic was used to form an NFS, a hybrid intelligent system that was implemented via a local linear model tree algorithm. For milk yield the correlations between EBV and EBV predicted by the ANN and NFS were 0.92 and 0.93, respectively. Corresponding correlations for fat yield were 0.93 and 0.93, respectively. Correlations between multitrait predictions of EBVs for milk and fat yield when predicted simultaneously by ANN were 0.93 and 0.93, respectively, whereas corresponding correlations with reference EBV for multitrait NFS were 0.94 and 0.95, respectively, for milk and fat production

Kinetics of cytokine receptor trafficking determine signaling and functional selectivity

Cytokines activate signaling via assembly of cell surface receptors, but it is unclear whether modulation of cytokine-receptor binding parameters can modify biological outcomes. We have engineered IL-6 variants with different affinities to gp130 to investigate how cytokine receptor binding dwell-times influence functional selectivity. Engineered IL-6 variants showed a range of signaling amplitudes and induced biased signaling, with changes in receptor binding dwell-times affecting more profoundly STAT1 than STAT3 phosphorylation. We show that this differential signaling arises from defective translocation of ligand-gp130 complexes to the endosomal compartment and competitive STAT1/STAT3 binding to phospho-tyrosines in gp130, and results in unique patterns of STAT3 binding to chromatin. This leads to a graded gene expression response and differences in ex vivo differentiation of Th17, Th1 and Treg cells. These results provide a molecular understanding of signaling biased by cytokine receptors, and demonstrate that manipulation of signaling thresholds is a useful strategy to decouple cytokine functional pleiotropy

Investigating Nanoscale Electron Transfer Processes at the Cell-Mineral Interface in Cobalt-Doped Ferrihydrite Using Geobacter sulfurreducens: A Multi-Technique Approach

This is the final version. Available from Frontiers Media via the DOI in this record.DATA AVAILABILITY STATEMENT: The raw data supporting the conclusion of this article will be made available by the authors, without undue reservation.Cobalt is an essential element for life and plays a crucial role in supporting the drive to clean energy, due to its importance in rechargeable batteries. Co is often associated with Fe in the environment, but the fate of Co in Fe-rich biogeochemically-active environments is poorly understood. To address this, synchrotron-based scanning X-ray microscopy (SXM) was used investigate the behaviour of cobalt at the nanoscale in Co-Fe(III)-oxyhydroxides undergoing microbial reduction. SXM can assess spatial changes in metal speciation and organic compounds helping to elucidate the electron transfer processes occurring at the cell-mineral interface and inform on the fate of cobalt in redox horizons. G. sulfurreducens was used to reduce synthetic Co-ferrihydrite as an analogue of natural cobalt-iron-oxides. Magnetite [Fe(II)/Fe(III)3O4] production was confirmed by powder X-ray diffraction (XRD), SXM and X-ray magnetic circular dichroism (XMCD) data, where best fits of the latter suggested Co-bearing magnetite. Macro-scale XAS techniques suggested Co(III) reduction occurred and complementary SXM at the nanoscale, coupled with imaging, found localised biogenic Co(III) reduction at the cell-mineral interface via direct contact with outer membrane cytochromes. No discernible localised changes in Fe speciation were detected in the reordered cobalt-iron-oxides that were formed and at the end point of the experiment only 11% Co and 1.5% Fe had been solubilised. The solid phase retention, alongside the highly localised and preferential cobalt bioreduction observed at the nanoscale is consistent with retention of Co in redox zones. This work improves our fundamental molecular-scale understanding of the fate of Co in complex environmental systems and supports the development of biogenic Co-doped magnetite for industrial applications from drug delivery systems to magnetic recording media.Natural Environment Research CouncilEPSRC studentshi

Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants

Cys2-His2 zinc finger proteins (ZFPs) are the largest group of transcription factors in higher metazoans. A complete characterization of these ZFPs and their associated target sequences is pivotal to fully annotate transcriptional regulatory networks in metazoan genomes. As a first step in this process, we have characterized the DNA-binding specificities of 129 zinc finger sets from Drosophila using a bacterial one-hybrid system. This data set contains the DNA-binding specificities for at least one encoded ZFP from 70 unique genes and 23 alternate splice isoforms representing the largest set of characterized ZFPs from any organism described to date. These recognition motifs can be used to predict genomic binding sites for these factors within the fruit fly genome. Subsets of fingers from these ZFPs were characterized to define their orientation and register on their recognition sequences, thereby allowing us to define the recognition diversity within this finger set. We find that the characterized fingers can specify 47 of the 64 possible DNA triplets. To confirm the utility of our finger recognition models, we employed subsets of Drosophila fingers in combination with an existing archive of artificial zinc finger modules to create ZFPs with novel DNA-binding specificity. These hybrids of natural and artificial fingers can be used to create functional zinc finger nucleases for editing vertebrate genomes