All and only CpG containing sequences are enriched in promoters abundantly bound by RNA polymerase II in multiple tissues

<p>Abstract</p> <p>Background</p> <p>The promoters of housekeeping genes are well-bound by RNA polymerase II (RNAP) in different tissues. Although the promoters of these genes are known to contain CpG islands, the specific DNA sequences that are associated with high RNAP binding to housekeeping promoters has not been described.</p> <p>Results</p> <p>ChIP-chip experiments from three mouse tissues, liver, heart ventricles, and primary keratinocytes, indicate that 94% of promoters have similar RNAP binding, ranging from well-bound to poorly-bound in all tissues. Using all 8-base pair long sequences as a test set, we have identified the DNA sequences that are enriched in promoters of housekeeping genes, focusing on those DNA sequences which are preferentially localized in the proximal promoter. We observe a bimodal distribution. Virtually all sequences enriched in promoters with high RNAP binding values contain a CpG dinucleotide. These results suggest that only transcription factor binding sites (TFBS) that contain the CpG dinucleotide are involved in RNAP binding to housekeeping promoters while TFBS that do not contain a CpG are involved in regulated promoter activity. Abundant 8-mers that are preferentially localized in the proximal promoters and exhibit the best enrichment in RNAP bound promoters are all variants of six known CpG-containing TFBS: ETS, NRF-1, BoxA, SP1, CRE, and E-Box. The frequency of these six DNA motifs can predict housekeeping promoters as accurately as the presence of a CpG island, suggesting that they are the structural elements critical for CpG island function. Experimental EMSA results demonstrate that methylation of the CpG in the ETS, NRF-1, and SP1 motifs prevent DNA binding in nuclear extracts in both keratinocytes and liver.</p> <p>Conclusion</p> <p>In general, TFBS that do not contain a CpG are involved in regulated gene expression while TFBS that contain a CpG are involved in constitutive gene expression with some CpG containing sequences also involved in inducible and tissue specific gene regulation. These TFBS are not bound when the CpG is methylated. Unmethylated CpG dinucleotides in the TFBS in CpG islands allow the transcription factors to find their binding sites which occur only in promoters, in turn localizing RNAP to promoters.</p

Combining morphological and genomic evidence to resolve species diversity and study speciation processes of the Pallenopsis patagonica (Pycnogonida) species complex

Background: Pallenopsis patagonica (Hoek, 1881) is a morphologically and genetically variable sea spider species whose taxonomic classification is challenging. Currently, it is considered as a species complex including several genetic lineages, many of which have not been formally described as species. Members of this species complex occur on the Patagonian and Antarctic continental shelves as well as around sub-Antarctic islands. These habitats have been strongly influenced by historical large-scale glaciations and previous studies suggested that communities were limited to very few refugia during glacial maxima. Therefore, allopatric speciation in these independent refugia is regarded as a common mechanism leading to high biodiversity of marine benthic taxa in the high-latitude Southern Hemisphere. However, other mechanisms such as ecological speciation have rarely been considered or tested. Therefore, we conducted an integrative morphological and genetic study on the P. patagonica species complex to i) resolve species diversity using a target hybrid enrichment approach to obtain multiple genomic markers, ii) find morphological characters and analyze morphometric measurements to distinguish species, and iii) investigate the speciation processes that led to multiple lineages within the species complex. Results: Phylogenomic results support most of the previously reported lineages within the P. patagonica species complex and morphological data show that several lineages are distinct species with diagnostic characters. Two lineages are proposed as new species, P. aulaeturcarum sp. nov. Dömel & Melzer, 2019 and P. obstaculumsuperavit sp. nov. Dömel, 2019, respectively. However, not all lineages could be distinguished morphologically and thus likely represent cryptic species that can only be identified with genetic tools. Further, morphometric data of 135 measurements showed a high amount of variability within and between species without clear support of adaptive divergence in sympatry. Conclusions: We generated an unprecedented molecular data set for members of the P. patagonica sea spider species complex with a target hybrid enrichment approach, which we combined with extensive morphological and morphometric analyses to investigate the taxonomy, phylogeny and biogeography of this group. The extensive data set enabled us to delineate species boundaries, on the basis of which we formally described two new species. No consistent evidence for positive selection was found, rendering speciation in allopatric glacial refugia as the most likely model of speciation

Experimental identification and in silico prediction of bacterivory in green algae

While algal phago-mixotrophs play a major role in aquatic microbial food webs, their diversity remains poorly understood. Recent studies have indicated several species of prasinophytes, early diverging green algae, to be able to consume bacteria for nutrition. To further explore the occurrence of phago-mixotrophy in green algae, we conducted feeding experiments with live fluorescently labeled bacteria stained with CellTracker Green CMFDA, heat-killed bacteria stained with 5-(4,6-dichlorotriazin-2-yl) aminofluorescein (DTAF), and magnetic beads. Feeding was detected via microscopy and/or flow cytometry in five strains of prasinophytes when provided with live bacteria: Pterosperma cristatum NIES626, Pyramimonas parkeae CCMP726, Pyramimonas parkeae NIES254, Nephroselmis pyriformis RCC618, and Dolichomastix tenuilepis CCMP3274. No feeding was detected when heat-killed bacteria or magnetic beads were provided, suggesting a strong preference for live prey in the strains tested. In parallel to experimental assays, green algal bacterivory was investigated using a gene-based prediction model. The predictions agreed with the experimental results and suggested bacterivory potential in additional green algae. Our observations underline the likelihood of widespread occurrence of phago-mixotrophy among green algae, while additionally highlighting potential biases introduced when using prey proxy to evaluate bacterial ingestion by algal cells. © 2021, The Author(s).National Science FoundationOpen access articleThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Electronic structure of underdoped cuprates

We consider a two-dimensional Fermi liquid coupled to low-energy commensurate spin fluctuations. At small coupling, the hole Fermi surface is large and centered around $Q =(\pi,\pi)$. We show that as the coupling increases, the shape of the quasiparticle Fermi surface and the spin-fermion vertex undergo a substantial evolution. At strong couplings, $g \gg \omega_0$, where $\omega_0$ is the upper cutoff in the spin susceptibility, the hole Fermi surface consists of small pockets centered at $(\pm \pi/2, \pm \pi/2)$. Simultaneously, the full spin-fermion vertex is much smaller than the bare one, and scales nearly linearly with $|q-Q|$, where $q$ is the momentum of the susceptibility. At intermediate couplings, there exist both, a large hole Fermi surface centered at $(\pi,\pi)$, and four hole pockets, but the quasiparticle residue is small everywhere except for the pieces of the pockets which face the origin of the Brillouin zone. The relevance of these results for recent photoemission experiments in $YBCO$ and $Bi2212$ systems is discussed.Comment: 19 pages, RevTeX, 15 figures embedded in the text, submitted to Phys. Rep., ps-file is also available at http://lifshitz.physics.wisc.edu/www/morr/morr_homepage.htm

Characterization of fossilized relatives of the White Spot Syndrome Virus in genomes of decapod crustaceans

$\bf Background:$ The White Spot Syndrome Virus (WSSV) is an important pathogen that infects a variety of decapod species and causes a highly contagious disease in penaeid shrimps. Mass mortalities caused by WSSV have pronounced commercial impact on shrimp aquaculture. Until now WSSV is the only known member of the virus family Nimaviridae, a group with obscure phylogenetic affinities. Its isolated position makes WSSV studies challenging due to large number of genes without homology in other viruses or cellular organisms. $\bf Results:$ Here we report the discovery of an unusually large amount of sequences with high similarity to WSSV in a genomic library from the Jamaican bromeliad crab $\textit {Metopaulias depressus}$. $\textit {De novo}$ assembly of these sequences allowed for the partial reconstruction of the genome of this endogenized virus with total length of 200 kbp encompassed in three scaffolds. The genome includes at least 68 putative open reading frames with homology in WSSV, most of which are intact. Among these, twelve orthologs of WSSV genes coding for non-structural proteins and nine genes known to code for the major components of the WSSV virion were discovered. Together with reanalysis of two similar cases of WSSV-like sequences in penaeid shrimp genomic libraries, our data allowed comparison of gene composition and gene order between different lineages related to WSSV. Furthermore, screening of published sequence databases revealed sequences with highest similarity to WSSV and the newly described virus in genomic libraries of at least three further decapod species. Analysis of the viral sequences detected in decapods suggests that they are less a result of contemporary WSSV infection, but rather originate from ancestral infection events. Phylogenetic analyses suggest that genes were acquired repeatedly by divergent viruses or viral strains of the Nimaviridae. $\bf Conclusions:$ Our results shed new light on the evolution of the Nimaviridae and point to a long association of this viral group with decapod crustaceans

Additional data for: Bar-Shalom et al, Light utilization in rhodopsin containing marine Verrucomicrobia: from their genomic blueprints to their phototrophic phenotypes

Additional supporting data generated as part of the bioinformatic pipeline: https://github.com/BejaLab/pelagisphaera</p

The complete mitochondrial genome of a cryptic amphipod species from the Gammarus fossarum complex. Supplementary Material

Supplementary material to the paper: Macher JN, Leese F, Weigand AM, Rozenberg A (2017) The complete mitochondrial genome of a cryptic amphipod species from the Gammarus fossarum complex. Mitochondrial DNA Part B, in print<br><br>methods.pdf<br>Supplementary methods<br><br>gene_sequences.zip<br>Untrimmed CDSs of 13 mitochondrial protein-coding genes of 12 amphipod species<br><br>cds_alignment.meg<br>Trimmed, concatenated and partitioned CDS alignment of 13 mitochondrial protein-coding genes of 12 amphipod species<br

Developments in Micro Ultrasonic Machining (MUSM)

International audienceUltrasonic machining (USM) presents a particular interest for the cutting of non-conductive, brittle materials such as ceramics, glasses or fused silica and quartz crystal. Unlike other non-traditional processes such Electrical Discharge Machining (EDM and micro-EDM, adapted to conductive materials), laser ablation or wet chemical etching, USM does not thermally damage the workpiece and does not create significant levels of stresses. Production of complex 3-D shapes with a volume of a few cubic millimeters is presented

The Generalization of the Conjunctive Rule for Aggregating Contradictory Sources of Information Based on Generalized Credal Sets

Abstract In the paper we consider the generalization of the conjunctive rule in the theory of imprecise probabilities. Let us remind that the conjunction rule, produced on credal sets, gives their intersection and it is not defined if this intersection is empty. In the last case the sources of information are called contradictory 1 . Meanwhile, in the Dempster-Shafer theory it is possible to use the conjunctive rule for contradictory sources of information having as a result a nonnormalized belief function that can be greater than zero at empty set. In the paper we try to exploit this idea and introduce into consideration so called generalized credal sets allowing to model imprecision (non-specificity), conflict, and contradiction in information. Based on generalized credal sets the conjunctive rule is well defined for contradictory sources of information and it can be conceived as the generalization of the conjunctive rule for belief functions. We also show how generalized credal sets can be used for modeling information when the avoiding sure loss condition is not satisfied, and consider coherence conditions and natural extension based on generalized credal sets

Implementation of Attribute Metadata with Application to Data Mining

Contents 1 Introduction 1 1.1 Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.2 Motivation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 2 User&apos;s Manual on Attribute Metadata 3 2.1 Getting Started . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 2.2 System Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 2.2.1 pr Command . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 2.2.2 sd and sr Commands . . . . . . . . . . . . . . . . . . . . . . . . . . 7 2.2.3 srd Command . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 2.2.4 dd and dr Commands . . . . . . . . . . . . . . . . . . . . . . . . . . 9 2.2.5 debug Command . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 2.2.6 input Command . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 2.3 Declaration of Attribute and Universal Data Types . . . . . . . . . . . . . . . . . . . . . . . . . . .