scholarly journals Coping with Tissue Sampling in Suboptimal Conditions: Comparison of Different Tissue Preservation Methods for Histological and Molecular Analysis

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 649
Author(s):  
Arturo Nicoletti ◽  
Paola Pregel ◽  
Laura Starvaggi Cucuzza ◽  
Francesca Tiziana Cannizzo ◽  
Alessandra Sereno ◽  
...  

A high quality of samples is crucial for the success of the analysis and diagnostic purposes, and therefore the right method of conservation is vitally important for an optimal preservation of tissues. Indeed, the time to deliver the sample to the laboratory could be remarkably long, especially under suboptimal conditions, and the use of specific fixatives or cold storage may not be possible. Moreover, the portability and cost of storage equipment, their toxicity, and their ease of use play a central role when choosing the correct preservation method. The aim of this study was the identification of a reliable and economic method for tissue preservation, to be used in “in-field” sampling, suitable for both histological and molecular analysis. Punch biopsies were collected from six cattle livers. Comparisons among methods of preservation using RNAlater, silica beads, and under-vacuum was carried out. These methods were tested through considering different times and temperatures, assuming three days as a maximum time interval from sampling to laboratory and choosing 4 °C and 24 °C as references for refrigeration temperature and room temperature, respectively. Histologically, the integrity of nucleus, cytoplasm, preservation of liver structure, and easiness of recognition of inflammatory infiltrate were evaluated. The integrity of the extracted DNA and RNA was evaluated through PCR and by means of an automated electrophoresis station, respectively. RNAlater and silica beads poorly preserved the histological parameters evaluated, independently from the temperature. Conversely, the vacuum-sealed samples showed a good grade of preservation until 48 h. DNA quality was acceptable for each sample. RNA integrity showed promising results only for samples preserved with silica beads.

2008 ◽  
Vol 62 (5) ◽  
pp. 429-434 ◽  
Author(s):  
A Gazziero ◽  
V Guzzardo ◽  
E Aldighieri ◽  
A Fassina

Background:Fixation is a chemical or physical procedure to prevent the degradation of proteins and tissue morphology. To optimise molecular analysis of archival tissues, it is essential that fixation preserves morphology along with protein epitopes and DNA/RNA integrity.Methods:A new formalin-free alcoholic-based fixative, FineFIX, was used to fix 15 serous effusions and 38 fine-needle aspirates, and cellular morphology and nucleic acid quality were evaluated.Results:The cytomorphology of the effusions and fine-needle aspirates obtained with FineFIX fixation was similar to that obtained with formalin-fixed counterparts. Immunocytochemistry showed comparable results with the traditional fixative, but FineFIX preserved higher-molecular-mass DNA and RNA, as demonstrated by successful PCR of large amplification products of >2000 bp.Conclusions:The formalin-free fixative produced not only satisfactory results for immunocytochemistry on cytological smears and cell blocks, but also excellent preservation of DNA and RNA, which can also be efficiently used for sophisticated molecular techniques.


2021 ◽  
Vol 11 (13) ◽  
pp. 6047
Author(s):  
Soheil Rezaee ◽  
Abolghasem Sadeghi-Niaraki ◽  
Maryam Shakeri ◽  
Soo-Mi Choi

A lack of required data resources is one of the challenges of accepting the Augmented Reality (AR) to provide the right services to the users, whereas the amount of spatial information produced by people is increasing daily. This research aims to design a personalized AR that is based on a tourist system that retrieves the big data according to the users’ demographic contexts in order to enrich the AR data source in tourism. This research is conducted in two main steps. First, the type of the tourist attraction where the users interest is predicted according to the user demographic contexts, which include age, gender, and education level, by using a machine learning method. Second, the correct data for the user are extracted from the big data by considering time, distance, popularity, and the neighborhood of the tourist places, by using the VIKOR and SWAR decision making methods. By about 6%, the results show better performance of the decision tree by predicting the type of tourist attraction, when compared to the SVM method. In addition, the results of the user study of the system show the overall satisfaction of the participants in terms of the ease-of-use, which is about 55%, and in terms of the systems usefulness, about 56%.


2021 ◽  
Vol 58 (1) ◽  
pp. 42-67 ◽  
Author(s):  
Mads Stehr ◽  
Anders Rønn-Nielsen

AbstractWe consider a space-time random field on ${{\mathbb{R}^d} \times {\mathbb{R}}}$ given as an integral of a kernel function with respect to a Lévy basis with a convolution equivalent Lévy measure. The field obeys causality in time and is thereby not continuous along the time axis. For a large class of such random fields we study the tail behaviour of certain functionals of the field. It turns out that the tail is asymptotically equivalent to the right tail of the underlying Lévy measure. Particular examples are the asymptotic probability that there is a time point and a rotation of a spatial object with fixed radius, in which the field exceeds the level x, and that there is a time interval and a rotation of a spatial object with fixed radius, in which the average of the field exceeds the level x.


Author(s):  
Anna Igorevna Filimonova

After the collapse of the USSR, fundamentally new phenomena appeared on the world arena, which became a watershed separating the bipolar order from the monopolar order associated with the establishment of the US global hegemony. Such phenomena were the events that are most often called «revolutions» in connection with the scale of the changes being made — «velvet revolutions» in the former Eastern Bloc, as well as revolutions of a different type, which ended in a change in the current regimes with such serious consequences that we are also talking about revolutionary transformations. These are technologies of «color revolutions» that allow organizing artificial and seemingly spontaneous mass protests leading to the removal of the legitimate government operating in the country and, in fact, to the seizure of power by a pro-American forces that ensure the Westernization of the country and the implementation of "neoliberal modernization", which essentially means the opening of national markets and the provision of natural resources for the undivided use of the Western factor (TNC and TNB). «Color revolutions» are inseparable from the strategic documents of the United States, in which, from the end of the 20th century, even before the collapse of the USSR, two main tendencies were clearly traced: the expansion of the right to unilateral use of force up to a preemptive strike, which is inextricably linked with the ideological justification of «missionary» American foreign policy, and the right to «assess» the internal state of affairs in countries and change it to a «democratic format», that is, «democratization». «Color revolutions», although they are not directly mentioned in strategic documents, but, being a «technical package of actions», straightforwardly follow from the right, assigned to itself by Washington, to unilateral use of force, which is gradually expanding from exclusively military actions to a comprehensive impact on an opponent country, i.e. essentially a hybrid war. Thus, the «color revolutions» clearly fit into the strategic concept of Washington on the use of force across the entire spectrum (conventional and unconventional war) under the pretext of «democratization». The article examines the period of registration and expansion of the US right to use force (which, according to the current international law, is a crime without a statute of limitations) in the time interval from the end of the twentieth century until 2014, filling semantic content about the need for «democratic transformations» of other states, with which the United States approached the key point of the events of the «Arab spring» and «color revolutions» in the post-Soviet space, the last and most ambitious of which was the «Euromaidan» in Ukraine in 2014. The article presents the material for the preparation of lectures and seminars in the framework of the training fields «International Relations» and «Political Science».


2015 ◽  
Vol 87 (4) ◽  
pp. 2217-2228 ◽  
Author(s):  
DAIANE M. DRESCH ◽  
TATHIANA E. MASETTO ◽  
SILVANA P.Q. SCALON

The aim of this study was to evaluate the sensitivity of Campomanesia adamantium seeds to desiccation by drying in activated silica gel (fast) and under laboratory conditions (slow). To assess the sensitivity of the seeds to desiccation, we used drying with silica gel and drying under laboratory conditions (25 °C), in order to obtain seeds with moisture content of 45, 35, 30, 25, 20, 15, 10 and 5%. The physiological potential of the seeds after desiccation was evaluated by measuring primary root protrusion, percentage of normal seedlings, germination seed index, seedling length, total seedling dry mass, electrical conductivity and DNA and RNA integrities. The C. adamantium seeds were sensitive to desiccation and to a reduction in moisture content to 21.1% or less by desiccation using silica gel, and to 17.2% or less by desiccation under laboratory conditions; impairment of the physiological potential of the seeds was observed at these low moisture content levels. The integrity of the seed genomic DNA was not affected after drying seeds in the two methods. However, drying in silica gel to 4.5% moisture content and drying under laboratory conditions to 5.4% moisture content resulted in the loss of seed RNA integrity.


Author(s):  
Olha Chernukha ◽  
Yurii Bilushchak

On the basis of mathematical model of convectivediffusion in a three-layered filter it is formulated a contactinitial-boundary value problem for description of mass transferof pollution accompanying the sorption processes. It is proposedthe algorithm for establishing the estimation of values of soughtfunction (concentration of pollution) at the lower boundary of thefilter on the basis of the interpolation of experimental data. It istaken into account that the right end of the interpolation segmentis unknown. It is determined the exact solutions of contact-initialboundaryvalue problems of mass transfer with provision forboth diffusive and convective mechanisms of transfer as well assorption processes, which is based on integral transformationsover space variables in the contacting regions. Is it designedsoftware and established regularities of convective diffusionprocess in the three-layered filter.


2001 ◽  
Vol 114 (10) ◽  
pp. 1797-1798
Author(s):  
K. Plant

Essential Molecular Biology, Vol. 1, 2nd edn edited by T. A. Brown Oxford University Press (2000) 240 pages. ISBN 0–19-963642-7 pound29.95 I have heard it said (though not to my face) that practical molecular biology is somewhat akin to cookery, and I have to admit (though not to my fellow Molecular Biologists) that there is an element of truth in this. Of course, our ovens are cooler, and our pie dishes smaller, but often it is a case of mixing ingredients in the right proportions and baking at 37 degrees C for an hour. In this book Brown becomes the Delia Smith of molecular biology, starting with how to boil an egg, before proceeding to more complex recipes. It is utterly and unashamedly aimed at the complete novice. As more and more branches of biology use molecular techniques, and as a constant flow of graduates take up the yoke of research, there will always be a demand for this type of manual. Of course, it is possible to find variants of a lot of these methods on the Internet, but, as these often include only the protocol, the complete novice is probably better off with a specifically designed manual. Another option is to go for the kit approach, but, in the same way as opening a tin of beans doesn't make you a chef, I whole heartedly agree with Brown when he says, ‘do not get the idea that using kits is the same as being a molecular biologist.’ In most branches of biology a bit of genuine molecular expertise can only enhance one's future job prospects! One of the things I liked about this book is its no-nonsense style, particularly those chapters written by the Editor. There is plenty of sound advice, not just on the molecular techniques but on how to be a good scientist in general. Although the advice starts with the basics, it isn't patronising to those experienced in other fields. One piece of advice that particularly tickled me was that, if your hand is too unsteady to load a gel, you should give up caffeine; I'm not sure whether the pain would be worth the gain! The first chapter deals with all the basic issues, from planning (not just how to do it, but is it worthy of your time, which is something we should all think about occasionally) to safety (which nasties you'll be using, what precautions to take, with internet sites referenced to fill in the details) and what equipment you'll need to run the experiments. In a nutshell, the rest of the book deals with microbiology for molecular biologists and molecular biology for everyone else. This includes DNA and RNA isolation, electrophoresis and cloning (generating, propagating and identifying recombinant DNA molecules, not the Dolly-the-sheep variety). There is a second volume to the set, which (based on the contents of the first edition) should cover making and screening libraries, the polymerase chain reaction, sequencing and gene expression studies. Bear in mind that to get very far you will need to buy the second volume, which is not yet published. It has been more than a decade since the first edition of this well-known and respected manual was published; so one would think its first update is about due. However, compared with the first edition, most chapters have very few changes. This is probably in the nature of such a basic manual - for example, good microbial practice doesn't change much. Only a couple of chapters have been extensively rewritten; those describing DNA extraction now include more recent resin-based methods. So to the crux of the matter: would I recommend buying it? Well, if you're a complete novice with little backup, I definitely think it is worth investing in a decent manual, and this one does have a nice comfortable feel to it. If you've already got a copy of the previous edition and are wondering whether to upgrade, I would say that the few improvements in these very basic techniques do not really make it worth spending the pound30 that this volume costs. That said, I rather suspect that the second volume, which deals with more complex techniques, will show far more technical advances and should complete your progression from culinary incompetence to cordon bleu.


2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Alida M. Bailleul ◽  
Jingmai O’Connor ◽  
Zhiheng Li ◽  
Qian Wu ◽  
Tao Zhao ◽  
...  

AbstractThe remains of ovarian follicles reported in nine specimens of basal birds represents one of the most remarkable examples of soft-tissue preservation in the Early Cretaceous Jehol Biota. This discovery was immediately contested and the structures alternatively interpreted as ingested seeds. Fragments of the purported follicles preserved in an enantiornithine (STM10-12) were extracted and subjected to multiple high-resolution analyses. The structures in STM10-12 possess the histological and histochemical characteristics of smooth muscles fibers intertwined together with collagen fibers, resembling the contractile structure in the perifollicular membrane (PFM) of living birds. Fossilized blood vessels, very abundant in extant PFMs, are also preserved. Energy Dispersive Spectroscopy shows the preserved tissues primarily underwent alumino-silicification, with minor mineralization via iron oxides. No evidence of plant tissue was found. These results confirm the original interpretation as follicles within the left ovary, supporting the interpretation that the right ovary was functionally lost early in avian evolution.


2020 ◽  
Vol 32 (5) ◽  
pp. 3401-3409
Author(s):  
Tom Wijers ◽  
Alwin Hylkema ◽  
Tsjippie Visser ◽  
Klaas Timmermans

Abstract Using either freshly pulped or preserved seaweed biomass for the extraction of protein can have a great effect on the amount of protein that can be extracted. In this study, the effect of four preservation techniques (frozen, freeze-dried, and air-dried at 40 and 70 °C) on the protein extractability, measured as Kjeldahl nitrogen, of four seaweed species, Chondrus crispus (Rhodophyceae), Ascophyllum nodosum, Saccharina latissima (both Phaeophyceae) and Ulva lactuca (Chlorophyceae), was tested and compared with extracting freshly pulped biomass. The effect of preservation is species dependent: in all four seaweed species, a different treatment resulted in the highest protein extractability. The pellet (i.e., the non-dissolved biomass after extraction) was also analyzed as in most cases the largest part of the initial protein ended up in the pellet and not in the supernatant. Of the four species tested, freeze-dried A. nodosum yielded the highest overall protein extractability of 59.6% with a significantly increased protein content compared with the sample before extraction. For C. crispus extracting biomass air-dried at 40 °C gave the best results with a protein extractability of 50.4%. Preservation had little effect on the protein extraction for S. latissima; only air-drying at 70 °C decreased the yield significantly. Over 70% of the initial protein ended up in the pellet for all U. lactuca extractions while increasing the protein content significantly. Extracting freshly pulped U. lactuca resulted in a 78% increase in protein content in the pellet while still containing 84.5% of the total initial total protein. These results show the importance of the right choice when selecting a preservation method and seaweed species for protein extraction. Besides the extracted protein fraction, the remaining pellet also has the potential as a source with an increased protein content.


Author(s):  
Aydın Buluç ◽  
John R Gilbert

This paper presents a scalable high-performance software library to be used for graph analysis and data mining. Large combinatorial graphs appear in many applications of high-performance computing, including computational biology, informatics, analytics, web search, dynamical systems, and sparse matrix methods. Graph computations are difficult to parallelize using traditional approaches due to their irregular nature and low operational intensity. Many graph computations, however, contain sufficient coarse-grained parallelism for thousands of processors, which can be uncovered by using the right primitives. We describe the parallel Combinatorial BLAS, which consists of a small but powerful set of linear algebra primitives specifically targeting graph and data mining applications. We provide an extensible library interface and some guiding principles for future development. The library is evaluated using two important graph algorithms, in terms of both performance and ease-of-use. The scalability and raw performance of the example applications, using the Combinatorial BLAS, are unprecedented on distributed memory clusters.


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