Search results for "sequence"

2020

AbstractDeveloping methods for accurate detection of RNA modifications remains a major challenge in epitranscriptomics. Next-generation sequencing-based mapping approaches have recently emerged but, often, they are not quantitative and lack specificity. Pseudouridine (ψ), produced by uridine isomerization, is one of the most abundant RNA modification. ψ mapping classically involves derivatization with soluble carbodiimide (CMCT), which is prone to variation making this approach only semi-quantitative. Here, we developed ‘HydraPsiSeq’, a novel quantitative ψ mapping technique relying on specific protection from hydrazine/aniline cleavage. HydraPsiSeq is quantitative because the obtained sign…

Draft genome sequences of Vibrio vulnificus strains recovered from moribund tilapia

2021

Potentially zoonotic Vibrio vulnificus strains were isolated from vibriosis outbreaks occurring on eastern Mediterranean tilapia farms between 2016 and 2019. In this work, the draft genome sequences of three representative isolates are presented.

MAGA: A Supervised Method to Detect Motifs From Annotated Groups in Alignments

2020

Multiple sequence alignments are usually phylogenetically driven. They are studied in the framework of evolution. But sometimes, it is interesting to study residue conservation at positions unconstrained by evolutionary rules. We present a supervised method to access a layer of information difficult to appreciate visually when many protein sequences are aligned. This new tool (MAGA; http://cbdm-01.zdv.uni-mainz.de/~munoz/maga/ ) locates positions in multiple sequence alignments differentially conserved in manually defined groups of sequences.

1H, 13C, and 15N NMR chemical shift assignment of the complex formed by the first EPEC EspF repeat and N-WASP GTPase binding domain

2021

AbstractLEE-encoded effector EspF (EspF) is an effector protein part of enteropathogenic Escherichia coli’s (EPEC’s) arsenal for intestinal infection. This intrinsically disordered protein contains three highly conserved repeats which together compose over half of the protein’s complete amino acid sequence. EPEC uses EspF to hijack host proteins in order to promote infection. In the attack EspF is translocated, together with other effector proteins, to host cell via type III secretion system. Inside host EspF stimulates actin polymerization by interacting with Neural Wiskott-Aldrich syndrome protein (N-WASP), a regulator in actin polymerization machinery. It is presumed that EspF acts by di…

Association of liver steatosis with lipid oversecretion and hypotriglyceridaemia in C57BL/6j mice fed trans-10, cis-12-linoleic acid

2003

AbstractConjugated linoleic acids (CLA) have recently been recognized to reduce body fat and plasma lipids in some animals. This study demonstrated that the steatosis accompanying the fat loss induced by trans-10,cis-12-C18:2 (CLA2) and not cis-9,trans-11-C18:2 (CLA1) isomer in C57BL/6j mice was not due to an alteration of the liver lipoprotein production that was even increased. The 3-fold decrease in plasma triacylglycerol contents and the induction of mRNA expression of low-density lipoprotein receptors concomitantly observed in CLA2-fed mice suggested an increase in the lipoprotein clearance at the level of the liver itself. CLA1 feeding produced similar but attenuated effects on trigly…

Drawing conclusions about what co-participants know: Knowledge-probing question–answer sequences in new employee orientation lectures

2019

This study aims to uncover the processes of interaction through which knowledge acquisition in new employee orientation is monitored and controlled. Using video-recordings of orientation lectures as data, the study focuses on question–answer sequences in which the lecturer’s question probes into the state of the employees’ knowledge; in particular, it looks at the third turn of the sequence, in which the lecturer comes to a conclusion concerning the participants’ knowledge. This is shown to be an unavoidably practical accomplishment, which is contingent on both the often ambivalent responses of the participants and the design of the knowledge-probing question. Also, the lecturer orients to…

Charitable food aid in Finland: from a social issue to an environmental solution

2019

Since the establishment of the first food bank in 1995, charitable food aid (CFA) has become entrenched in Finland as a seemingly irreplaceable solution to food poverty. Further, it has recently been suggested that the focus of food aid activities is shifting from food poverty and temporary hunger alleviation towards environmental sustainability through addressing food waste via organized re-distribution of expiring food from retail to charitable organizations. This potentially creates a mechanism that (1) solidifies food poverty and (2) fortifies the paradoxical situation where charitable organizations delivering food aid are dependent on food waste rather than trying to reduce it. To unde…

Spatio-temporal deixis and cognitive models in early Indo-European

2018

AbstractThis paper is a comparative study based on the linguistic evidence in Vedic Sanskrit and Homeric Greek, aimed at reconstructing the space-time cognitive models used in the Proto-Indo-European language in a diachronic perspective. While it has been widely recognized that ancient Indo-European languages construed earlier (and past) events as in front of later ones, as predicted in the Time-Reference-Point mapping, it is less clear how in the same languages the passage took place from this ‘archaic’ Time-RP model or non-deictic sequence, in which future events are behind or follow the past ones in a temporal sequence, to the more recent ‘post-archaic’ Ego-RP model that is found only fr…

Direct Observation of Nanometer-Scale Pores of Melittin in Supported Lipid Monolayers

2015

Melittin is the most studied membrane-active peptide and archetype within a large and diverse group of pore formers. However, the molecular characteristics of melittin pores remain largely unknown. Herein, we show by atomic force microscopy (AFM) that lipid monolayers in the presence of melittin are decorated with numerous regularly shaped circular pores that can be distinguished from nonspecific monolayer defects. The specificity of these pores is reinforced through a statistical evaluation of depressions found in Langmuir-Blodgett monolayers in the presence and absence of melittin, which eventually allows characterization of the melittin-induced pores at a quantitative low-resolution leve…

Reactions of the hydrofluoroborate salts of open-chain analogues of Reissert compounds with some α,β-ethylenic esters

1999

The reaction of the hydrofluoroborate salt of an open-chain analogue of a Reissert compound with some α,β-ethylenic esters does not give a [4 + 2] cycloadduct, as previously described in the case of ethyl acrylate. The reaction starts with a 1,3-dipolar cycloaddition of a munchnone imine 5c, d. The [3 + 2] cycloadducts 13 evolve via a rearrangement–condensation sequence to give a substituted 2-pyridone derivative 18 or 19. The proposed mechanism has been verified by the isolation and structural X-ray analysis of some compounds of the reaction sequence.