Search results for "assembly"

Variable-order reference-free variant discovery with the Burrows-Wheeler Transform

2020

Abstract Background In [Prezza et al., AMB 2019], a new reference-free and alignment-free framework for the detection of SNPs was suggested and tested. The framework, based on the Burrows-Wheeler Transform (BWT), significantly improves sensitivity and precision of previous de Bruijn graphs based tools by overcoming several of their limitations, namely: (i) the need to establish a fixed value, usually small, for the order k, (ii) the loss of important information such as k-mer coverage and adjacency of k-mers within the same read, and (iii) bad performance in repeated regions longer than k bases. The preliminary tool, however, was able to identify only SNPs and it was too slow and memory con…

Transcriptomic Changes Following Partial Depletion of CENP-E in Normal Human Fibroblasts

2021

The centromere is a fundamental chromosome structure in which the macro-molecular kinetochore assembles and is bound by spindle microtubules, allowing the segregation of sister chromatids during mitosis. Any alterations in kinetochore assembly or functioning or kinetochore–microtubule attachments jeopardize chromosome stability, leading to aneuploidy, a common feature of cancer cells. The spindle assembly checkpoint (SAC) supervises this process, ensuring a faithful segregation of chromosomes. CENP-E is both a protein of the kinetochore and a crucial component of the SAC required for kinetochore–microtubule capture and stable attachment, as well as congression of chromosomes to the metaphas…

Fluorescent Nanowires Self-Assembled through Host-Guest Interactions in Modified Calcein

2011

Inside Cover: Fluorescent Nanowires Self-Assembled through Host-Guest Interactions in Modified Calcein (Angew. Chem. Int. Ed. 32/2011)

2011

Molecular Self-Assembly Versus Surface Restructuring During Calcite Dissolution.

2016

Organic additives are known to alter the mineral-water interface in various ways. On the one hand, organic molecules can self assemble into ordered structures wetting the surface. On the other hand, their presence can affect the interfacial morphology, referred to as surface restructuring. Here, we investigate the impact, of a class of calcium-complexing azo dyes on the dissolution of calcite (10.4) using high-resolution atomic force microscopy operated in aqueous solution, with a focus on the two constitutional isomers Eriochrome Black T and Eriochrome Black A. A very pronounced surface restructuring is observed in the presence of the dye solution, irrespective of the specific dye used and…

Where Is the Most Hydrophobic Region? Benzopurpurine Self-Assembly at the Calcite–Water Interface

2017

Control of molecular self-assembly at solid–liquid interfaces is challenging due to the complex interplay between molecule–molecule, molecule–surface, molecule–solvent, surface–solvent, and solvent–solvent interactions. Here, we use in-situ dynamic atomic force microscopy to study the self-assembly of Benzopurpurine 4B into oblong islands with a highly ordered inner structure yet incommensurate with the underlying calcite (10.4) surface. Molecular dynamics and free energy calculations provide insights by showing that Benzopurpurine 4B molecules do not anchor to the surface directly but instead assemble on top of the second hydration layer. This seemingly peculiar behavior was then rationali…

Mercaptophenol-Protected Gold Colloids as Nuclei for the Crystallization of Inorganic Minerals:  Templated Crystallization on Curved Surfaces

1999

The self-assembly of monolayers of thiols on gold(111) surfaces yields substrates that are able to template in a controlled manner, the nucleation and growth of crystals of calcium carbonate from solution. In the absence of additives, various factors such as the nature of the thiol, the temperature, and the pH are now established as influencing the nature and relative amounts of the different CaCO3 phases (calcite, vaterite, and aragonite). Recently, we have been able to extend the use of thiol/gold self-assembled monolayers as templates for the growth of inorganic crystals by utilizing protected gold colloids instead of flat gold surfaces. The thiol monolayers that protect the colloids pro…

Oligodendroglioma cells synthesize the differentiation-specific linker histone H1˚ and release it into the extracellular environment through shed ves…

2013

Chromatin remodelling can be involved in some of the epigenetic modifications found in tumor cells. One of the mechanisms at the basis of chromatin dynamics is likely to be synthesis and incorporation of replacement histone variants, such as the H1° linker histone. Regulation of the expression of this protein can thus be critical in tumorigenesis. In developing brain, H1° expression is mainly regulated at the post-transcriptional level and RNA-binding proteins (RBPs) are involved. In the past, attention mainly focused on the whole brain or isolated neurons and little information is available on H1° expression in other brain cells. Even less is known relating to tumor glial cells. In this st…

Subcellular localization of bacteriophage PRD1 proteins in Escherichia coli

2014

Bacteria possess an intricate internal organization resembling that of the eukaryotes. The complexity is especially prominent at the bacterial cell poles, which are also known to be the preferable sites for some bacteriophages to infect. Bacteriophage PRD1 is a well-known model serving as an ideal system to study structures and functions of icosahedral internal membrane-containing viruses. Our aim was to analyze the localization and interactions of individual PRD1 proteins in its native host Escherichia coli. This was accomplished by constructing a vector library for production of fluorescent fusion proteins. Analysis of solubility and multimericity of the fusion proteins, as well as their …

Cation binding resorcinarene bis-crowns: the effect of lower rim alkyl chain length on crystal packing and solid lipid nanoparticles

2012

A group of seven resorcinarene bis-crown ethers (CNBC5) with two polyether bridges at the upper rim and either propyl, butyl, pentyl, heptyl, nonyl, decyl or undecyl groups at the lower rim were synthesized and their binding properties with Cs+ were investigated by NMR titration. The bis-crowns form 1:2 complexes with Cs+ with binding constants of logK 4–5. Crystal structures of bis-crowns and their Cs+ and K+ complexes were studied and different packing motifs were found depending on the alkyl chain length. Short ethyl, propyl and butyl alkyl chains gave a layer or pillar packing where the polar and non-polar regions cannot be distinguished, whereas longer pentyl and decyl chains formed bi…