scholarly journals Ultra-parallel ChIP-seq by barcoding of intact nuclei

2018 ◽  
Author(s):  
L. Arrigoni ◽  
H. Al-Hasani ◽  
F. Ramírez ◽  
I. Panzeri ◽  
D.P Ryan ◽  
...  

AbstractChromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is an invaluable tool for mapping chromatin-associated proteins. However, sample preparation is still a largely individual and labor-intensive process that hinders assay throughput and comparability. Here, we present a novel method for ultra-parallelized high-throughput ChIP-seq that addresses the aforementioned problems. The method, called RELACS (Restriction Enzyme-based Labeling of Chromatin in Situ), employs barcoding of chromatin within intact nuclei extracted from different sources (e.g. tissues, treatments, time points). Barcoded nuclei are pooled and processed within the same ChIP, for maximal comparability and significant workload reduction. The choice of user-friendly, straightforward, enzymatic steps for chromatin fragmentation and barcoding makes RELACS particularly suitable for implementation large-scale clinical studies and scarce samples. RELACS can generate ChIP-seq libraries from hundreds of samples within three days and with less than 1000 cells per sample.

2021 ◽  
Vol 13 (2) ◽  
pp. 320
Author(s):  
José P. Granadeiro ◽  
João Belo ◽  
Mohamed Henriques ◽  
João Catalão ◽  
Teresa Catry

Intertidal areas provide key ecosystem services but are declining worldwide. Digital elevation models (DEMs) are important tools to monitor the evolution of such areas. In this study, we aim at (i) estimating the intertidal topography based on an established pixel-wise algorithm, from Sentinel-2 MultiSpectral Instrument scenes, (ii) implementing a set of procedures to improve the quality of such estimation, and (iii) estimating the exposure period of the intertidal area of the Bijagós Archipelago, Guinea-Bissau. We first propose a four-parameter logistic regression to estimate intertidal topography. Afterwards, we develop a novel method to estimate tide-stage lags in the area covered by a Sentinel-2 scene to correct for geographical bias in topographic estimation resulting from differences in water height within each image. Our method searches for the minimum differences in height estimates obtained from rising and ebbing tides separately, enabling the estimation of cotidal lines. Tidal-stage differences estimated closely matched those published by official authorities. We re-estimated pixel heights from which we produced a model of intertidal exposure period. We obtained a high correlation between predicted and in-situ measurements of exposure period. We highlight the importance of remote sensing to deliver large-scale intertidal DEM and tide-stage data, with relevance for coastal safety, ecology and biodiversity conservation.


2020 ◽  
Vol 8 (1) ◽  
pp. 53
Author(s):  
Thomas Oh ◽  
Jittiwat Sermsripong ◽  
Barry W. Hicks

Studies reporting quantitation and imaging of chlorophyll in corals using visible fluorescent emission in the red near 680 nm can suffer from competing emission from other red-emitting pigments. Here, we report a novel method of selectively imaging chlorophyll distributions in coral in situ using only the near infrared (NIR) fluorescence emission from chlorophyll. Commercially available equipment was assembled that allowed the sequential imaging of visible, visible-fluorescent, and NIR-fluorescent pigments on the same corals. The relative distributions of chlorophyll and fluorescent proteins (GFPs) were examined in numerous corals in the Caribbean Sea, the Egyptian Red Sea, the Indonesian Dampier Strait, and the Florida Keys. Below 2 m depth, solar induced NIR chlorophyll fluorescence can be imaged in daylight without external lighting, thus, it is much easier to do than visible fluorescence imaging done at night. The distributions of chlorophyll and GFPs are unique in every species examined, and while there are some tissues where both fluorophores are co-resident, often tissues are selectively enriched in only one of these fluorescent pigments. Although laboratory studies have clearly shown that GFPs can be photo-protective, their inability to prevent large scale bleaching events in situ may be due to their limited tissue distribution.


2018 ◽  
Vol 7 (2) ◽  
pp. 714
Author(s):  
Akshay Sabu ◽  
Nirmalakumar Rajamane

Geopolymer is an inorganic polymer, which can perform as an effective binder in place of Portland cement. With this, the Geopolymer concrete has become highly Ecofriendly with very low carbon footprint. The GPC formulation at present utilises industrial waste materials like fly ash and GGBS, which are activated with well-proportioned alkaline liquid. At present the commercially available lye and Sodium Silicate solution are used to prepare alkaline liquid capable of initiating geopolymer reaction. It is noticed that the liquid system has limited shelf life by making field production of Geopolymer concrete mixes was a difficult one more over the liquid system and its ingredients are difficult to transport over longer distances. This has been the main obstacle for development of large-scale applications of GPC mixes on commercial basis. This issue was addressed in the present study by using solid activator in replacement of liquid solution. The solid activating system can be produced just before the preparation of fresh GPC mixes at anyway at any time. It is found that the mechanical strength (40 – 45Mpa) property was similar to the liquid activating GPC mixes. This new technique of production of GPC mixes using solid activators can be consider as the major breakthrough for commercialization / large scale field applications of Geopolymer technology.


Author(s):  
Claudia Antonetti ◽  
Anna Maria Raspolli Galletti ◽  
Iginio Longo

The development of greener chemical processes is becoming more and more important because this approach moves towards sustainable methods and products, minimizing pollution and risks for human health and environment. In these perspectives, microwaves seem to fulfil these requirements; in this context, we have tested a novel method both for the synthesis of nanocatalysts and for thermal activation of catalytic reactions. Until now, microwave chemistry has been generally performed inside a closed metal cavity, i.e. a microwave oven, but this approach presents relevant drawbacks, in particular for large scale application. Recently, we have proposed a new, cheap, sustainable process for large scale preparation of nanocatalysts, overcoming the disadvantages of the current synthesis methods. This novel method has been successfully adopted for the preparation in situ of ruthenium, palladium and silver nanoparticles as colloids or on different supports. Our procedure is safe and cheap, enabling to obtain the utmost efficiency and control also for industrial application. The obtained nanocatalysts present small average diameters, good morphology and very narrow sizes distribution with an absolute reproducibility. The ruthenium nanocatalysts were tested in the selective hydrogenation of phenol to cyclohexanone and palladium nanocatalysts were tested in the selective hydrogenation of cinnamaldehyde to hydrocinnamaldehyde, and we obtained good performances in both reactions.


2022 ◽  
Vol 12 (2) ◽  
pp. 750
Author(s):  
Junyu Wang ◽  
Gordon Forbes ◽  
Elizaveta Forbes

Bubble size measurement is a vital part of flotation system analysis and diagnostics. This work evaluates a commercial camera probe as a novel method for in situ bubble size measurement. This device is compared to the conventional Anglo Platinum Bubble Sizer (Stone Three TM). It was found that, in laboratory applications, the in situ bubble size analysis technology appears to be a more user-friendly and reliable option for determining bubble size in flotation, whereas the Anglo Platinum Bubble Sizer is more applicable for full scale industrial work. This probe was then used to conduct a rigorous comparison of the behavior of different frother chemistries at a variety of background solution ionic strength conditions. The critical coalescence concentrations and the minimum Sauter mean bubble diameters were determined. Five frothers were compared in terms of their ability to reduce bubble size and sensitivity to salinity. In order to adjust plant recipe and control strategy accordingly, it is recommended that the plant would need to use less frother during periods of the high salinity of process water to achieve the minimum Sauter mean bubble size.


2021 ◽  
Vol 13 (13) ◽  
pp. 2523
Author(s):  
Piero Gili ◽  
Marco Civera ◽  
Rinto Roy ◽  
Cecilia Surace

The concept and preliminary design of an unmanned lighter-than-air (LTA) platform instrumented with different remote sensing technologies is presented. The aim is to assess the feasibility of using a remotely controlled airship for the land monitoring of medium sized (up to 107 m2) urban or rural areas at relatively low altitudes (below 1000 m) and its potential convenience with respect to other standard remote and in-situ sensing systems. The proposal includes equipment for high-definition visual, thermal, and hyperspectral imaging as well as LiDAR scanning. The data collected from these different sources can be then combined to obtain geo-referenced products such as land use land cover (LULC), soil water content (SWC), land surface temperature (LSC), and leaf area index (LAI) maps, among others. The potential uses for diffuse structural health monitoring over built-up areas are discussed as well. Several mission typologies are considered.


2017 ◽  
Vol 120 (3) ◽  
pp. 303-322
Author(s):  
D. Pienaar ◽  
B.M. Guy ◽  
C. Pienaar ◽  
K.S. Viljoen

Abstract Mineralogical and textural variability of ores from different sources commonly leads to processing inefficiencies, particularly when a processing plant is designed to treat ore from a single source (i.e. ore of a relatively uniform composition). The bulk of the Witwatersrand ore in the Klerksdorp goldfield, processed at the AngloGold Ashanti Great Noligwa treatment plant, is derived from the Vaal Reef (>90%), with a comparatively small contribution obtained from the Crystalkop Reef (or C-Reef). Despite the uneven contribution, it is of critical importance to ensure that the processing parameters are optimized for the treatment of both the Vaal and C-Reefs. This paper serves to document the results of a geometallurgical study of the C-Reef at the Great Noligwa gold mine in the Klerksdorp goldfield of South Africa, with the primary aim of assessing the suitability of the processing parameters that are in use at the Great Noligwa plant. The paper also draws comparisons between the C-Reef and the Vaal Reef A-facies (Vaal Reef) and attempts to explain minor differences in the recovery of gold and uranium from these two sources. Three samples of the C-Reef were collected in-situ from the underground operations at Great Noligwa mine for mineralogical analyses and metallurgical tests. Laboratory-scale leach tests for gold (cyanide) and uranium (sulphuric acid) were carried out using dissolution conditions similar to that in use at the Great Noligwa plant, followed by further diagnostic leaching in the case of gold. The gold in the ore was found to be readily leachable with recoveries ranging from 95% to 97% (as opposed to 89% to 93% for the Vaal Reef). Additional recoveries were achieved in the presence of excess cyanide (96% to 98%). The recovery of uranium varied between 72% and 76% (as opposed to 30% to 64% for the Vaal Reef), which is substantially higher than predicted, given the amount of brannerite in the ore, which is generally regarded as refractory. Thus, the higher uranium recoveries from the C-Reef imply that a proportion of the uranium was recovered by the partial dissolution of brannerite. As the Vaal Reef contain high amounts of chlorite (3% to 8%), which is an important acid consumer, it is considered likely that this could have reduced the effectiveness of the H2SO4 leach in the case of the ore of the Vaal Reef. Since the gold and uranium recoveries from the C-Reef were higher than the recoveries from the Vaal Reef, the results demonstrate that the processing parameters used for treatment of the Vaal Reef are equally suited to the treatment of the C-Reef. Moreover, small processing modifications, such as increased milling and leach retention times, may well increase the recovery of gold (particularly when e.g. coarse gold, or unexposed gold, is present).


2008 ◽  
Vol 59 (11) ◽  
Author(s):  
Iulia Lupan ◽  
Sergiu Chira ◽  
Maria Chiriac ◽  
Nicolae Palibroda ◽  
Octavian Popescu

Amino acids are obtained by bacterial fermentation, extraction from natural protein or enzymatic synthesis from specific substrates. With the introduction of recombinant DNA technology, it has become possible to apply more rational approaches to enzymatic synthesis of amino acids. Aspartase (L-aspartate ammonia-lyase) catalyzes the reversible deamination of L-aspartic acid to yield fumaric acid and ammonia. It is one of the most important industrial enzymes used to produce L-aspartic acid on a large scale. Here we described a novel method for [15N] L-aspartic synthesis from fumarate and ammonia (15NH4Cl) using a recombinant aspartase.


2018 ◽  
Vol 23 (suppl_1) ◽  
pp. e16-e16
Author(s):  
Ahmed Moussa ◽  
Audrey Larone-Juneau ◽  
Laura Fazilleau ◽  
Marie-Eve Rochon ◽  
Justine Giroux ◽  
...  

Abstract BACKGROUND Transitions to new healthcare environments can negatively impact patient care and threaten patient safety. Immersive in situ simulation conducted in newly constructed single family room (SFR) Neonatal Intensive Care Units (NICUs) prior to occupancy, has been shown to be effective in testing new environments and identifying latent safety threats (LSTs). These simulations overlay human factors to identify LSTs as new and existing process and systems are implemented in the new environment OBJECTIVES We aimed to demonstrate that large-scale, immersive, in situ simulation prior to the transition to a new SFR NICU improves: 1) systems readiness, 2) staff preparedness, 3) patient safety, 4) staff comfort with simulation, and 5) staff attitude towards culture change. DESIGN/METHODS Multidisciplinary teams of neonatal healthcare providers (HCP) and parents of former NICU patients participated in large-scale, immersive in-situ simulations conducted in the new NICU prior to occupancy. One eighth of the NICU was outfitted with equipment and mannequins and staff performed in their native roles. Multidisciplinary debriefings, which included parents, were conducted immediately after simulations to identify LSTs. Through an iterative process issues were resolved and additional simulations conducted. Debriefings were documented and debriefing transcripts transcribed and LSTs classified using qualitative methods. To assess systems readiness and staff preparedness for transition into the new NICU, HCPs completed surveys prior to transition, post-simulation and post-transition. Systems readiness and staff preparedness were rated on a 5-point Likert scale. Average survey responses were analyzed using dependent samples t-tests and repeated measures ANOVAs. RESULTS One hundred eight HCPs and 24 parents participated in six half-day simulation sessions. A total of 75 LSTs were identified and were categorized into eight themes: 1) work organization, 2) orientation and parent wayfinding, 3) communication devices/systems, 4) nursing and resuscitation equipment, 5) ergonomics, 6) parent comfort; 7) work processes, and 8) interdepartmental interactions. Prior to the transition to the new NICU, 76% of the LSTs were resolved. Survey response rate was 31%, 16%, 7% for baseline, post-simulation and post-move surveys, respectively. System readiness at baseline was 1.3/5,. Post-simulation systems readiness was 3.5/5 (p = 0.0001) and post-transition was 3.9/5 (p = 0.02). Staff preparedness at baseline was 1.4/5. Staff preparedness post-simulation was 3.3/5 (p = 0.006) and post-transition was 3.9/5 (p = 0.03). CONCLUSION Large-scale, immersive in situ simulation is a feasible and effective methodology for identifying LSTs, improving systems readiness and staff preparedness in a new SFR NICU prior to occupancy. However, to optimize patient safety, identified LSTs must be mitigated prior to occupancy. Coordinating large-scale simulations is worth the time and cost investment necessary to optimize systems and ensure patient safety prior to transition to a new SFR NICU.


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