scholarly journals Chromatin is frequently unknotted at the megabase scale

2019 ◽  
Author(s):  
Dimos Goundaroulis ◽  
Erez Lieberman Aiden ◽  
Andrzej Stasiak

Knots in the human genome would greatly impact diverse cellular processes ranging from transcription to gene regulation. To date, it has not been possible to directly examine the genome in vivo for the presence of knots. Recently, methods for serial fluorescent in situ hybridization have made it possible to measure the 3d position of dozens of consecutive genomic loci, in vivo. However, the determination of whether genomic trajectories are knotted remains challenging, because small errors in the localization of a single locus can transform an unknotted trajectory into a highly-knotted trajectory, and vice versa. Here, we use stochastic closure analysis to determine whether a genomic trajectory is knotted in the setting of experimental noise. We analyse 4727 deposited genomic trajectories of a 2Mb long chromatin interval from chromosome 21. For 243 of these trajectories, their knottedness could be reliably determined despite the possibility of localization errors. Strikingly, in each of these 243 cases, the trajectory was unknotted. We note a potential source of bias, insofar as knotted contours may be more difficult to reliably resolve. Nevertheless, our data is consistent with a model where, at the scales probed, the human genome is often free of knots.

RSC Advances ◽  
2016 ◽  
Vol 6 (110) ◽  
pp. 108635-108644 ◽  
Author(s):  
Xian-En Zhao ◽  
Yongrui He ◽  
Ping Yan ◽  
Na Wei ◽  
Renjun Wang ◽  
...  

In situ UA-DDLLME coupled with UHPLC-MS/MS has been developed for simultaneous determination of neurotransmitters and baicalein from Parkinson's disease rats.


Parasitology ◽  
2000 ◽  
Vol 120 (6) ◽  
pp. 547-551 ◽  
Author(s):  
O. BILLKER ◽  
A. J. MILLER ◽  
R. E. SINDEN

Malarial gametocytes circulate in the peripheral blood of the vertebrate host as developmentally arrested intra-erythrocytic cells, which only resume development into gametes when ingested into the bloodmeal of the female mosquito vector. The ensuing development encompasses sexual reproduction and mediates parasite transmission to the insect. In vitro the induction of gametogenesis requires a drop in temperature and either a pH increase from physiological blood pH (ca pH 7·4) to about pH 8·0, or the presence of a gametocyte-activating factor recently identified as xanthurenic acid (XA). However, it is unclear whether either the pH increase or XA act as natural triggers in the mosquito bloodmeal. We here use pH-sensitive microelectrodes to determine bloodmeal pH in intact mosquitoes. Measurements taken in the first 30 min after ingestion, when malarial gametogenesis is induced in vivo, revealed small pH increases from 7·40 (mouse blood) to 7·52 in Aedes aegypti and to 7·58 in Anophěles stephensi. However, bloodmeal pH was clearly suboptimal if compared to values required to induce gametogenesis in vitro. Xanthurenic acid is shown to extend the pH-range of exflagellation in vitro in a dose-dependent manner to values that we have observed in the bloodmeal, suggesting that in vivo malarial gametogenesis could be further regulated by both these factors.


2006 ◽  
Vol 100 (5) ◽  
pp. 1577-1583 ◽  
Author(s):  
Shawn E. Soutiere ◽  
Wayne Mitzner

Previous work by our group has demonstrated substantial differences in lung volume and morphometric parameters between inbred mice. Specifically, adult C3H/HeJ (C3) have a 50% larger lung volume and 30% greater mean linear intercept than C57BL/6J (B6) mice. Although much of lung development occurs postnatally in rodents, it is uncertain at what age the differences between these strains become manifest. In this study, we performed quasi-static pressure-volume curves and morphometric analysis on neonatal mice. Lungs from anesthetized mice were degassed in vivo using absorption of 100% O2. Pressure-volume curves were then recorded in situ. The lungs were then fixed by instillation of Zenker’s solution at a constant transpulmonary pressure. The left lung from each animal was used for morphometric determination of mean air space chord length ( Lma). We found that the lung volume of C3 mice was substantially greater than that of B6 mice at all ages. In contrast, there was no difference in Lma (62.7 μm in C3 and 58.5 μm in B6) of 3-day-old mice. With increasing age (8 days), there was a progressive decrease in the Lma of both strains, with the magnitude of the decrease in B6 Lma mice exceeding that of C3. C3 lung volume remained 50% larger. The combination of parenchymal architectural similarity with lung air volume differences and different rates of alveolar septation support the hypothesis that lung volume and alveolar dimensions are independently regulated.


2000 ◽  
Vol 04 (01) ◽  
pp. 1-7 ◽  
Author(s):  
W. Herzog ◽  
E. M. Hasler ◽  
T. R. Leonard

The purpose of this communication is to present an idea, and its technical implementation, on how to estimate experimentally in vivo joint contact pressure distributions. The idea is illustrated for the cat patellofemoral joint. For this particular joint, the approach requires muscle force and hindlimb movement measurements during unrestrained locomotion, and the quantification of the joint contact pressures in situ for conditions approximating the in vivo conditions as closely as possible. Although the approach is time-consuming and has its limitations, it is, as far as we know, the first purely experimental approach to determine the in vivo joint contact pressures during normal movement. "Purely experimental" refers to the idea that the required movements, muscle forces and contact pressures are all measured rather than estimated theoretically.


Reproduction ◽  
2009 ◽  
Vol 138 (1) ◽  
pp. 45-53 ◽  
Author(s):  
Xavier Druart ◽  
Juliette Cognié ◽  
Gérard Baril ◽  
Frédérique Clément ◽  
Jean-Louis Dacheux ◽  
...  

The fertility of ram semen after cervical insemination is substantially reduced by 24 h of storage in liquid form. The effects of liquid storage on the transit of ram spermatozoa in the ewe genital tract was investigated using a new procedure allowing direct observation of the spermatozoa in the genital tract. Ejaculated ram spermatozoa were double labeled with R18 and MitoTracker Green FM, and used to inseminate ewes in estrus either cervically through the vagina or laparoscopically into the base of the uterine horns. Four hours after insemination, the spermatozoa were directly observedin situusing fibered confocal fluorescence microscopy in the base, middle and tip of the uterine horns, the utero-tubal junction (UTJ) and the oviduct. The high resolution video images obtained with this technique allowed determination of the distribution of spermatozoa and individual motility in the lumen of the ewe's genital tract. The results showed a gradient of increasing concentration of spermatozoa from the base of the uterus to the UTJ 4 h after intra-uterine insemination into the base of the horns. The UTJ was shown to be a storage region for spermatozoa before their transfer to the oviduct. Thein vitrostorage of spermatozoa in liquid form decreased their migration through the cervix and reduced the proportion of motile spermatozoa and their straight line velocity at the UTJ and their transit into the oviduct.


Planta Medica ◽  
2018 ◽  
Vol 84 (11) ◽  
pp. 795-805
Author(s):  
Lucia Disch ◽  
Kristina Forsch ◽  
Beate Siewert ◽  
Jürgen Drewe ◽  
Gert Fricker

Abstract Petasites hybridus extract is used in the treatment of seasonal allergic rhinitis. The aim of this study was to evaluate the active constituent petasin and its isomers isopetasin and neopetasin (petasins) in the P. hybridus extract Ze 339 for liberation, dissolution, absorption, and metabolism. The determination of pH-dependent thermodynamic solubility was performed via the shake-flask method. Petasins exhibited a low solubility that was pH independent. In vivo, the concentration of solute drugs is decreased continuously by intestinal absorption. Therefore, low solubility is not assumed to be critical for in vivo performance. Additionally, dissolution of an herbal medicinal product containing P. hybridus extract Ze 339 was assessed. Furthermore, high permeability through Caco-2 monolayers was evident. Using an in situ rat model, absorption capacity for petasins was found in all tested intestinal segments, namely, duodenum, jejunum, and ileum. Besides, high metabolism was evident both in Caco-2 monolayers and in the rat intestine. To compare intestinal and hepatic metabolism of petasins, in vitro enzyme assays using liver and intestinal cytosol and microsomes (S9 fraction) of rats and humans were performed. A significantly higher metabolic rate was found in the liver S9 fraction of both species compared with the intestinal S9 fraction.


2006 ◽  
Vol 28 (7) ◽  
pp. 648-655 ◽  
Author(s):  
L. Garay ◽  
E.G. Ramos ◽  
E. Cardiel ◽  
R. Muñoz ◽  
P.R. Hernández

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