scholarly journals New protocol for successful isolation and amplification of DNA from exiguous fractions of specimens: a tool to overcome the basic obstacle in molecular analyses of myxomycetes

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8406 ◽  
Author(s):  
Paulina Janik ◽  
Michał Ronikier ◽  
Anna Ronikier
Keyword(s):  
Biological Material ◽  
Dna Isolation ◽  
Cost Effective ◽  
Biological Research ◽  
Herbarium Specimens ◽  
Direct Pcr ◽  
Phylogenetic Studies ◽  
Successful Isolation ◽  
Herbarium Collections ◽  
Non Destructive

Herbarium collections provide an essential basis for a wide array of biological research and, with development of DNA-based methods, they have become an invaluable material for genetic analyses. Yet, the use of such material is hindered by technical limitations related to DNA degradation and to quantity of biological material. The latter is inherent for some biological groups, as best exemplified by myxomycetes which form minute sporophores. It is estimated that ca. two-thirds of myxomycete taxa are represented by extremely scanty material. As DNA isolation methods applied so far in myxomycete studies require destructive sampling of many sporophores, a large part of described diversity of the group remains unavailable for phylogenetic studies or barcoding. Here, we tested several procedures of DNA isolation and amplification to seek for an efficient and possibly non-destructive method of sampling. Tests were based on herbarium specimens of 19 species representing different taxonomic orders. We assayed several variants of isolation based on silica gel membrane columns, and a newly designed procedure using highly reduced amount of biological material (small portion of spores), based on fine disruption of spores and direct PCR. While the most frequently used column-based method led to PCR success in 89.5% of samples when a large amount of material was used, its performance dropped to 52% when based on single sporophores. Single sporophores provided amplicons in 89.5% of samples when using a kit dedicated to low-amount DNA samples. Our new procedure appeared the most effective (94.7%) while it used only a small fraction of spores, being nearly non-destructive; it was also the most cost-effective. We thus demonstrate that combination of adequate handling of spore micro-disruption coupled with application of direct PCR can be an efficient way to circumvent technical limitations for genetic studies in myxomycetes and thus can substantially improve taxon sampling for phylogeny and barcoding. Additionally, this approach gives a unique possibility to apply both molecular and morphological assays to the same structure (sporophore), which then can be further stored as documentation.

scholarly journals Rapid high throughput template preparation (rHTTP) method: a novel cost effective method of direct PCR for a wide range of plants

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Prassan Choudhary ◽  
Sudipta Das ◽  
Hillol Chakdar ◽  
Arjun Singh ◽  
Sanjay Kumar Goswami ◽  
...  
Keyword(s):  
Ssr Markers ◽  
High Throughput ◽  
Field Experiments ◽  
Dna Isolation ◽  
Cost Effective ◽  
Direct Pcr ◽  
Rice Varieties ◽  
Plant Materials ◽  
Wide Range ◽  
Commercial Kits

Abstract Background Conventional plant DNA isolation methods are complex, time consuming and require technical expertise. These limitations were overcome using the DNA isolation kits which, however significantly add to the research costs. Hence the present study was aimed to develop a high throughput, rapid and inexpensive method of PCR ready DNA template preparation from plant materials. Methods Concentration of SDS in lysis buffer, amount of starting material, period and temperature for lysis were optimized for obtaining PCR ready templates from plant materials. The method was tested using RAPD and ITS specific primers for different plant species like rice, wheat, mustard, pea, soybean, pigeonpea, tomato, maize, march lilly, bougainvillea, Indian blanket flower, nerium, petunia, purple pirouette petunia, moses-in-the-cradle, golden cane palm, duranta, periwinkle, chrysanthemum and two xerophytes viz. Dipterygium glaucum and Crotaleria burhia. SSR markers RM18398 and RM26108 showed successful amplification in rice varieties Improved Pusa Basmati 1 and KS Dev 12. The effectiveness of the method was tested using fresh as well as 1 year old tissues. The storability of the lysate was also tested. Results In this report, we developed a novel method called rapid high throughput template preparation (rHTTP) method to prepare PCR ready DNA templates. Most striking feature of this technique is that it can be done anywhere where water can be boiled by any means. Using rHTTP method, PCR ready templates can be prepared in just 10 min. Robust and reproducible amplification for all the test plants were recorded with RAPD, plant ITS primers and SSR markers following this method. rHTTP methods works well for both fresh as well as old plant tissues. The lysates had a shelf life of 1 month when stored at 4 °C and 3 days when stored at room temperature. Conclusions rHTTP method has several advantages over the other protocols like ease of execution, no requirement of tissue grinding/liquid nitrogen/hazardous chemicals and above all, equally effective for both fresh and old samples. Using this method, costs per prep comes down ~ 10–50 times as compared to most commercial kits. This method can be used for on-field experiments like molecular diagnostics, varietal identification etc.

Duplex DNA barcoding allows accurate species determination of morphologically similar limpets (Patella spp.) from non-destructive sampling

2016 ◽  
Vol 97 (7) ◽  
pp. 1479-1482 ◽  
Author(s):  
Thomas J. Ashton ◽  
Meriem Kayoueche-Reeve ◽  
Andrew J. Blight ◽  
Jon Moore ◽  
David M. Paterson
Keyword(s):  
Dna Barcoding ◽  
Species Abundance ◽  
Microscopic Analysis ◽  
Cost Effective ◽  
Field Studies ◽  
Similar Species ◽  
Species Determination ◽  
Destructive Sampling ◽  
Species Specific ◽  
Non Destructive

Accurate discrimination of two morphologically similar species of Patella limpets has been facilitated by using qPCR amplification of species-specific mitochondrial genomic regions. Cost-effective and non-destructive sampling is achieved using a mucus swab and simple sample lysis and dilution to create a PCR template. Results show 100% concurrence with dissection and microscopic analysis, and the technique has been employed successfully in field studies. The use of highly sensitive DNA barcoding techniques such as this hold great potential for improving previously challenging field assessments of species abundance.

scholarly journals Indigenous vascular plants of the Soutpansberg, South Africa

Bothalia ◽  
2019 ◽  
Vol 49 (1) ◽  
Author(s):  
Norbert Hahn
Keyword(s):  
South Africa ◽  
Conservation Planning ◽  
Vascular Plants ◽  
Biosphere Reserve ◽  
Herbarium Specimens ◽  
Mountain Range ◽  
Floristic Diversity ◽  
Literature Reviews ◽  
The Status ◽  
Herbarium Collections

Background: The first checklist for the Soutpansberg was published in 1946, and the second list was compiled by the author in 2006 as part of his doctoral thesis. Currently, there is a need for an updated account of the biodiversity of the Soutpansberg Centre of Endemism and Diversity for conservation planning in the Vhembe Biosphere Reserve, within which the Soutpansberg is the principle geomorphological feature.Objectives: To present an updated list of vascular plants recorded for the Soutpansberg.Method: The list was compiled from various sources including literature reviews, herbarium specimens, herbarium databases and personal observations.Results: This article presents the most geographically accurate and taxonomically updated list of the indigenous vascular flora of the Soutpansberg, the northernmost mountain range of South Africa. Altogether 2443 taxa are recorded belonging to 922 genera in 187 families and 64 orders.Conclusion: The list presented in this article confirms the status of the Soutpansberg as a centre of floristic diversity in southern Africa. Notable is the higher-order diversity of the flora. It is likely that both future surveys and reviews of herbarium collections will add new taxa to the current total.

scholarly journals Propagation of Dry Habitat Fern Species Using Spore Collections from Historic Herbarium Specimens

2011 ◽  
pp. 43-54
Author(s):  
Gunnar Ovstebo
Keyword(s):  
Royal Botanic Garden ◽  
Herbarium Specimens ◽  
Botanic Garden ◽  
Spore Viability ◽  
Living Plant ◽  
Herbarium Material ◽  
Plant Collection ◽  
Fern Species ◽  
Herbarium Collections ◽  
Horticultural Research

Spores sourced from historic herbarium specimens have been used to introduce wild-collected material to the Royal Botanic Garden Edinburgh (RBGE) living plant collection. The ability of dry habitat ferns to maintain spore viability for prolonged periods makes it possible to grow plants from the historically important RBGE herbarium collections. The factors that affect the ability of spores to germinate from herbarium collections are described. Three fern species from the Pteridaceae – Actiniopteris semiflabellata, Anogramma leptophylla and Aleuritopteris scioana – which were not previously in cultivation at RBGE were germinated from herbarium material of different ages. Germination was observed from all three species. Plants produced in this experiment were accessed into the RBGE living plant collection for future horticultural research and germination trials.

An efficient protocol for the isolation of fungal DNA for strains obtained from oil contaminated fields

2012 ◽  
Vol 2 (4) ◽  
pp. 162-165
Author(s):  
Bhavya Ravi ◽  
Madhulika Rai ◽  
Sandhya Mehrotra ◽  
Rajesh Mehrotra
Keyword(s):  
Contaminated Soils ◽  
Petroleum Hydrocarbons ◽  
Dna Isolation ◽  
Cost Effective ◽  
Industrial Applications ◽  
Glass Beads ◽  
Natural Ecosystem ◽  
Dna Yield ◽  
Genomic Study ◽  
Fungal Dna

A natural ecosystem contaminated with petroleum hydrocarbons is likely to favor the growth of taxonomically diverse microbes having the ability to degrade these organic compounds. They can be exploited for purposes like bioremediation of oil contaminated soils and to obtain enzymes like lipases having important industrial applications. In this paper, a novel “IBG” (Improved ‘Bust and Grab’) protocol has been reported for the isolation of fungal DNA from strains collected from oil contaminated fields. Conventional methods for DNA isolation from fungi require the use of enzymes, liquid nitrogen, glass beads etc. The method reported here circumvents the use of enzymes or glass beads and is cost effective and can be used while handling large number of samples. The DNA yield obtained by the IBG protocol is significant and of good quality. The good quality DNA isolated by IBG protocol can be used for the quick and cost effective isolation of fungal genomic DNA facilitating the genomic study of microbes obtained from oil contaminated fields.

scholarly journals Estimating the age and mechanism of boulder transport related with extreme waves using lichenometry

2020 ◽  
Vol 44 (6) ◽  
pp. 870-897
Author(s):  
Maria A Oliveira ◽  
Esteve Llop ◽  
César Andrade ◽  
Cristina Branquinho ◽  
Ronald Goble ◽  
...  
Keyword(s):  
Age Estimation ◽  
Alternative Explanation ◽  
Estimation Method ◽  
Cost Effective ◽  
Optically Stimulated Luminescence ◽  
Extreme Waves ◽  
Non Destructive ◽  
Boulder Deposits ◽  
Lichen Growth

Tsunamis and storms cause considerable coastal flooding, numerous fatalities, destruction of structures, and erosion. The characterization of energy and frequency associated with each wave contribute to the risk assessment in coastal regions. Coastal boulder deposits represent a physical proof of extreme inundation and allow us to study the effects of marine floods further back in time than instrumental and historical records. Age estimation of these deposits is challenging due to lack of materials (such as sand, shells, corals, or organic matter) that retain information about the passage of time. Lichenometry, a simple age estimation method, which is cost-effective, quick to apply, and non-destructive, is here proposed as a solution. A lichen growth model for a calcium-tolerant lichen species was developed and used to estimate the age of a boulder deposit related to extreme marine inundation(s) in Portugal. Estimated ages indicate several very recent events (<700 years) for most of the boulders’ stabilization and agree with results obtained with optically stimulated luminescence of marine sands found beneath boulders. Frequent and recent boulder transport implies a storm-origin for this deposit. These conclusions contrast with other works describing identical deposits that are attributed to paleotsunamis. This study presents a methodology using lichenometry as a successful alternative for age estimation in rocky coastal settings. These results offer an alternative explanation for coastal boulder deposits found on the west coast of Portugal.

scholarly journals Real-time structural health monitoring for concrete beams: a cost-effective ‘Industry 4.0’ solution using piezo sensors

2020 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Arka Ghosh ◽  
David John Edwards ◽  
M. Reza Hosseini ◽  
Riyadh Al-Ameri ◽  
Jemal Abawajy ◽  
...  
Keyword(s):  
Structural Health Monitoring ◽  
Real Time ◽  
Health Monitoring ◽  
Industry 4.0 ◽  
Concrete Beams ◽  
Low Cost ◽  
Cost Effective ◽  
Content Type ◽  
Structural Health ◽  
Non Destructive

PurposeThis research paper adopts the fundamental tenets of advanced technologies in industry 4.0 to monitor the structural health of concrete beam members using cost-effective non-destructive technologies. In so doing, the work illustrates how a coalescence of low-cost digital technologies can seamlessly integrate to solve practical construction problems.Design/methodology/approachA mixed philosophies epistemological design is adopted to implement the empirical quantitative analysis of “real-time” data collected via sensor-based technologies streamed through a Raspberry Pi and uploaded onto a cloud-based system. Data was analysed using a hybrid approach that combined both vibration-characteristic-based method and linear variable differential transducers (LVDT).FindingsThe research utilises a novel digital research approach for accurately detecting and recording the localisation of structural cracks in concrete beams. This non-destructive low-cost approach was shown to perform with a high degree of accuracy and precision, as verified by the LVDT measurements. This research is testament to the fact that as technological advancements progress at an exponential rate, the cost of implementation continues to reduce to produce higher-accuracy “mass-market” solutions for industry practitioners.Originality/valueAccurate structural health monitoring of concrete structures necessitates expensive equipment, complex signal processing and skilled operator. The concrete industry is in dire need of a simple but reliable technique that can reduce the testing time, cost and complexity of maintenance of structures. This was the first experiment of its kind that seeks to develop an unconventional approach to solve the maintenance problem associated with concrete structures. This study merges industry 4.0 digital technologies with a novel low-cost and automated hybrid analysis for real-time structural health monitoring of concrete beams by fusing several multidisciplinary approaches into one integral technological configuration.

scholarly journals A Cost-Effective System for Aerial 3D Thermography of Buildings

2020 ◽  
Vol 6 (8) ◽  
pp. 76
Author(s):  
Claudia Daffara ◽  
Riccardo Muradore ◽  
Nicola Piccinelli ◽  
Nicola Gaburro ◽  
Tullio de Rubeis ◽  
...  
Keyword(s):  
3D Imaging ◽  
Three Dimensional ◽  
Cost Effective ◽  
Complex Structures ◽  
Non Destructive Testing ◽  
Ir Thermography ◽  
Destructive Testing ◽  
Effective System ◽  
Reconstruction Software ◽  
Non Destructive

Three-dimensional (3D) imaging and infrared (IR) thermography are powerful tools in many areas in engineering and sciences. Their joint use is of great interest in the buildings sector, allowing inspection and non-destructive testing of elements as well as an evaluation of the energy efficiency. When dealing with large and complex structures, as buildings (particularly historical) generally are, 3D thermography inspection is enhanced by Unmanned Aerial Vehicles (UAV—also known as drones). The aim of this paper is to propose a simple and cost-effective system for aerial 3D thermography of buildings. Special attention is thus payed to instrument and reconstruction software choice. After a very brief introduction to IR thermography for buildings and 3D thermography, the system is described. Some experimental results are given to validate the proposal.

The potential for the use of herbarium specimens to determine the host plants of Ceutorhynchus (Coleoptera: Curculionidae)

2015 ◽  
Vol 148 (4) ◽  
pp. 493-498 ◽  
Author(s):  
David R. Gillespie ◽  
Beth I. Gillespie
Keyword(s):  
Biological Control ◽  
North America ◽  
Host Plant ◽  
Host Plants ◽  
Herbarium Specimens ◽  
Plant Associations ◽  
Control Programmes ◽  
Herbarium Collections ◽  
Developing Knowledge

AbstractThe host plants of native Ceutorhynchus Germar (Coleoptera: Curculionidae) species are poorly known in North America, and knowledge of these is essential for biological control programmes involving this genus of weevils. We hypothesised that weevil larva emergence holes on plant specimens in herbarium collections might reveal potential plant-insect associations, and help locate populations of hosts for non-target testing. We examined 1114 plant specimens in 16 genera and 60 species of Brassicaceae and found 70 specimens among 30 species that showed evidence of feeding injury and exit holes typical of Ceutorhynchus. We used this information to locate populations of two species of Ceutorhynchus. Herbarium collections may be useful tools for developing knowledge of host plant associations for species of Ceutorhynchus.

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