From STRs to SNPs via ddRAD-seq: geographic assignment of confiscated tortoises at reduced costs

Assigning individuals to their source populations is crucial for conservation research, especially for endangered species threatened by illegal trade and translocations. Genetic assignment can be achieved with different types of molecular markers, but technical advantages and cost saving are recently promoting the shift from short tandem repeats (STRs) to single nucleotide polymorphisms (SNPs). Here, we designed, developed, and tested a small panel of SNPs for cost-effective geographic assignment of individuals with unknown origin of the endangered Mediterranean tortoise Testudo hermanni. We started by performing a ddRAD-seq experiment on 70 wild individuals of T. hermanni from 38 locations. Results obtained using 3,182 SNPs are comparable to those previously obtained using STR markers in terms of genetic structure and power to identify the macro-area of origin. However, our SNPs revealed further insights into the substructure in Western populations, especially in Southern Italy. A small panel of highly informative SNPs was then selected and tested by genotyping 190 individuals using the KASP genotyping chemistry. All the samples from wild populations of known geographic origin were genetically re-assigned with high accuracy to the original population. This reduced SNPs panel represents an efficient molecular tool that enables individuals to be genotyped at low cost (less than €15 per sample) for geographical assignment and identification of hybrids. This information is crucial for the management in-situ of confiscated animals and their possible re-allocation in the wild. Our methodological pipeline can easily be extended to other species.

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Application of Epoxy Resin for Improvement of the Banana Stem-Acoustic Panel

Recent Innovations in Chemical Engineering (Formerly Recent Patents on Chemical Engineering) ◽

10.2174/2405520415666211229125344 ◽

2021 ◽

Vol 15 ◽

Author(s):

Mohd Azril Riduan ◽

Mohd Jumain Jalil ◽

Intan Suhada Azmi ◽

Afifudin Habulat ◽

Danial Nuruddin Azlan Raofuddin ◽

...

Keyword(s):

Oleic Acid ◽

Kinetic Modelling ◽

Low Cost ◽

Cost Effective ◽

Performic Acid ◽

High Yield ◽

Renewable Materials ◽

Runge Kutta Method ◽

To Come

Background: Greener epoxidation by using vegetable oil to create an eco-friendly epoxide is being studied because it is a more cost-effective and environmentally friendly commodity that is safer than non-renewable materials. The aim of this research is to come up with low-cost solutions for banana trunk acoustic panels with kinetic modelling of epoxy-based palm oil. Method: In this study, the epoxidation of palm oleic acid was carried out by in situ performic acid to produce epoxidized palm oleic acid. Results: Banana trunk acoustic panel was successfully innovated based on the performance when the epoxy was applied. Lastly, a mathematical model was developed by using the numerical integration of the 4th order Runge-Kutta method, and the results showed that there is a good agreement between the simulation and experimental data, which validates the kinetic model. Conclusion: Overall, the peracid mechanism was effective in producing a high yield of epoxy from palm oleic acid that is useful for the improvement of acoustic panels based on the banana trunk.

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Re-establishment of an endangered subspecies: the Norfolk Island Boobook Owl Ninox novaeseelandiae undulata

Bird Conservation International ◽

10.1017/s0959270900001313 ◽

1996 ◽

Vol 6 (1) ◽

pp. 63-80 ◽

Cited By ~ 9

Author(s):

Penny D. Olsen

Keyword(s):

New Zealand ◽

Low Cost ◽

Female Offspring ◽

Nest Boxes ◽

Large Trees ◽

Island Group ◽

Norfolk Island ◽

In The Wild ◽

Original Female

SummaryThe Norfolk Island Boobook Ninox novaeseelandiae undulata is confined to the small, isolated Norfolk Island group, an Australian territory. On morphological and biogeographical grounds, it is here classified as a large, distinctive subspecies of the New Zealand Morepork N. novaeseelandiae. In 1986 only one specimen, a female, survived. A shortage of large trees with suitable nesting holes appeared to be the immediate problem. The Australian Nature Conservation Agency, islanders and New Zealand wildlife authorities have cooperated in an attempt to re-establish an owl population in situ. Nest-boxes were erected in trees in the area frequented by the female and were used readily as roosts. In September 1987, two male New Zealand Moreporks were introduced. The female paired with one male and produced four hybrid F offspring (in 1989 and 1990). Two of these paired in mid-1991 and have since produced five F offspring (two in 1993 and three in 1994). The original female remains paired but now appears to be reproductively senile. At present there seems to be a shortage of mature males, since two female offspring are paired and both lay eggs and attempt to incubate them in the same nest; and a lone female has established a territory. In early 1995 all eleven owls appeared to be alive in the wild. The effort is low-cost, requires relatively little manpower, is carried out with minimal disturbance to the owls, and goes hand in hand with other conservation programmes.

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A contribution to solve the arsenic problem in groundwater of Ganges Delta by in-situ treatment

Water Science & Technology ◽

10.2166/wst.2008.751 ◽

2008 ◽

Vol 58 (10) ◽

pp. 2009-2015 ◽

Cited By ~ 5

Author(s):

U. Rott ◽

H. Kauffmann

Keyword(s):

Arsenic Removal ◽

Low Cost ◽

Treatment Plant ◽

Cost Effective ◽

Treatment Technology ◽

Manganese Removal ◽

Arsenic In Groundwater ◽

Cost Effective Treatment ◽

Removal Of Arsenic

Arsenic in groundwater is a huge problem in numerous regions of the world. Many people are exposed to high arsenic concentrations and consequently risk getting ill or even die as a result of arsenic poisoning. There are several efficient technologies for the removal of arsenic but often these methods have disadvantages, e.g. high costs for installation and/or operation, the need for chemicals or the production of arsenic contaminated filter sludge. These disadvantages can make the application difficult, especially in poor regions. Under suitable ancillary conditions the subterranean (in-situ) treatment, which is often used for iron and manganese removal from groundwater, can also be applied for the removal of arsenic and can be a cost-effective treatment technology. A field trial was carried out with a low-cost in-situ treatment plant in West Bengal/India which is described in this paper, in order to investigate whether this treatment technology is also applicable under the boundary conditions there. As for the in-situ treatment technology besides oxygen no additives are required and no arsenic contaminated filter sludge is produced this technology could be a suitable method for arsenic removal especially in poor regions.

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Development of a Cost-Effective Sensing Platform for Monitoring Phosphate in Natural Waters

Chemosensors ◽

10.3390/chemosensors6040057 ◽

2018 ◽

Vol 6 (4) ◽

pp. 57 ◽

Cited By ~ 5

Author(s):

Andrew Donohoe ◽

Gareth Lacour ◽

Peter McCluskey ◽

Dermot Diamond ◽

Margaret McCaul

Keyword(s):

Natural Waters ◽

Limit Of Detection ◽

Low Cost ◽

Unit Cost ◽

High Standard ◽

Cost Effective ◽

Remote Access ◽

Sampling Location ◽

Sensing Platform

A sensing platform for the in situ, real-time analysis of phosphate in natural waters has been realised using a combination of microfluidics, colorimetric reagent chemistries, low-cost LED-based optical detection and wireless communications. Prior to field deployment, the platform was tested over a period of 55 days in the laboratory during which a total of 2682 autonomous measurements were performed (854 each of sample, high standard and baseline, and 40 × 3 spiked solution measurements). The platform was subsequently field-deployed in a freshwater stream at Lough Rea, Co., Galway, Ireland, to track changes in phosphate over a five day period. During this deployment, 165 autonomous measurements (55 each of sample, high standard, and baseline) were performed and transmitted via general packet radio service (GPRS) to a web interface for remote access. Increases in phosphate levels at the sampling location coincident with rainfall events (min 1.45 µM to max 10.24 µM) were detected during the deployment. The response was found to be linear up to 50 µM PO43−, with a lower limit of detection (LOD) of 0.09 µM. Laboratory and field data suggest that despite the complexity of reagent-based analysers, they are reasonably reliable in remote operation, and offer the best opportunity to provide enhanced in situ chemical sensing capabilities. Modifications that could further improve the reliability and scalability of these platforms while simultaneously reducing the unit cost are discussed.

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A Green Alternative for Aryl Iodide Preparation from Aromatic Amines

Current Organic Synthesis ◽

10.2174/1570179417666200203121437 ◽

2020 ◽

Vol 17 (2) ◽

pp. 131-135

Author(s):

Zohreh Shahnavaz ◽

Lia Zaharani ◽

Mohd Rafie Johan ◽

Nader Ghaffari Khaligh

Keyword(s):

Low Cost ◽

Cost Effective ◽

Raw Material ◽

Diazonium Salts ◽

Separation And Purification ◽

One Pot ◽

Aryl Iodide ◽

Aryl Iodides ◽

The One

Background: In continuation of our previous work and the applications of saccharin, we encouraged to investigate the one-pot synthesis of the aryl iodides by the diazotization of the arene diazonium saccharin salts. Objective: Arene diazonium salts play an important role in organic synthesis as intermediate and a wide variety of aromatic compounds have been prepared using them. A serious drawback of arene diazonium salts is their instability in a dry state; therefore, they must be stored and handled carefully to avoid spontaneous explosion and other hazard events. Methods: The arene diazonium saccharin salts were prepared as active intermediates in situ through the reaction of various aryl amines with tert-butyl nitrite (TBN) in the presence of saccharin (Sac–H). Then, in situ obtained intermediates were used into the diazotization step without separation and purification in the current protocol. Results: A variety of aryl iodides were synthesized at a greener and low-cost method in the presence of TBN, Sac–H, glacial acetic acid, and TEAI. Conclusion: In summary, a telescopic reaction is developed for the synthesis of aryl iodides. The current methodology is safe, cost-effective, broad substrate scope, and metal-free. All used reagents are commercially available and inert to moisture and air. Also, the saccharine and tetraethylammonium cation could be partially recovered from the reaction residue, which reduces waste generation, energy consumption, raw material, and waste disposal costs.

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Comparison of Low-Cost Methods for Soil Water Holding Capacity

10.21203/rs.3.rs-1181839/v1 ◽

2022 ◽

Author(s):

Prabhu Govindasamy ◽

Sonu Kumar Mahawer ◽

Jake Mowrer ◽

Muthukumar Bagavathiannan ◽

Mahendra Prasad ◽

...

Keyword(s):

Soil Water ◽

Analytical Methods ◽

Low Cost ◽

Cost Effective ◽

Clay Loam ◽

Sandy Clay Loam ◽

Sandy Clay ◽

Random Samples ◽

Water Measurement

Abstract Purpose: The use of cost-effective methods for measurement of WHC is common in underdeveloped and developing countries, but the accuracy of these cost-effective methods compared to the sophisticated and more expensive alternatives is unclear. Methods: To compare different WHC measurement methods, 30 random samples of clay loam and sandy clay loam soils of Jhansi, India were used. The methods compared here were: FAO in-situ method (FAO), Keen Raczkowski box method (KM), funnel method (FM), column method (CM) and pressure plate method (PPA). Results: For WHC measurements the PPA results were comparable to KM and FM methods for sandy clay loam, and KM and FAO methods for clay loam. Conclusion: Therefore, until a reliable method that matches the results of sophisticated analytical methods of soil water measurement is available, different inexpensive analytical methods can be used, but they must be chosen with caution. The findings from this study will facilitate appropriate selection of a suitable method.

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Enabling Image-Based Streamflow Monitoring at the Edge

Remote Sensing ◽

10.3390/rs12122047 ◽

2020 ◽

Vol 12 (12) ◽

pp. 2047 ◽

Cited By ~ 1

Author(s):

Fabio Tosi ◽

Matteo Rocca ◽

Filippo Aleotti ◽

Matteo Poggi ◽

Stefano Mattoccia ◽

...

Keyword(s):

Embedded System ◽

High Speed ◽

Low Cost ◽

Cost Effective ◽

Engineering Practice ◽

Embedded Devices ◽

Cloud Processing ◽

Internet Connections ◽

Processing Device

Monitoring streamflow velocity is of paramount importance for water resources management and in engineering practice. To this aim, image-based approaches have proved to be reliable systems to non-intrusively monitor water bodies in remote places at variable flow regimes. Nonetheless, to tackle their computational and energy requirements, offload processing and high-speed internet connections in the monitored environments, which are often difficult to access, is mandatory hence limiting the effective deployment of such techniques in several relevant circumstances. In this paper, we advance and simplify streamflow velocity monitoring by directly processing the image stream in situ with a low-power embedded system. By leveraging its standard parallel processing capability and exploiting functional simplifications, we achieve an accuracy comparable to state-of-the-art algorithms that typically require expensive computing devices and infrastructures. The advantage of monitoring streamflow velocity in situ with a lightweight and cost-effective embedded processing device is threefold. First, it circumvents the need for wideband internet connections, which are expensive and impractical in remote environments. Second, it massively reduces the overall energy consumption, bandwidth and deployment cost. Third, when monitoring more than one river section, processing “at the very edge” of the system efficiency improves scalability by a large margin, compared to offload solutions based on remote or cloud processing. Therefore, enabling streamflow velocity monitoring in situ with low-cost embedded devices would foster the widespread diffusion of gauge cameras even in developing countries where appropriate infrastructure might be not available or too expensive.

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Simple and cost-effective SNP genotyping method for discriminating subpopulations of the fish pathogen, Nocardia seriolae

10.1101/2021.12.28.474260 ◽

2021 ◽

Author(s):

Cuong Thanh Le ◽

Erin P Prince ◽

Derek S Sarovich ◽

Thu Thi Anh Nguyen ◽

Hung VuKhac ◽

...

Keyword(s):

Low Cost ◽

Bacterial Pathogen ◽

Cost Effective ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Putative Origin ◽

Nocardia Seriolae ◽

Mutation Assay ◽

Economic And Social Impacts ◽

Pathogen Surveillance

Nocardia seriolae has caused significant fish losses in Asia and the Americas in recent decades, including in Vietnam, which has witnessed devastating economic and social impacts due to this bacterial pathogen. Surveillance strategies are urgently needed to mitigate N. seriolae dissemination in Vietnamese aquaculture and mariculture industries. Whole-genome sequencing (WGS) offers the highest level of resolution to discriminate closely related strains and to determine their putative origin and transmission routes. However, WGS is impractical for epidemiological investigations and pathogen surveillance due to its time-consuming and costly nature, putting this technology out-of-reach for many industry end-users. To overcome this issue, we targeted two previously characterised, phylogenetically informative single-nucleotide polymorphisms (SNPs) in N. seriolae that accurately distinguish: i) Vietnamese from non-Vietnamese strains, and ii) the two Vietnamese subclades. Using the mismatch amplification mutation assay (MAMA) format, we developed assays that genotype strains based on differences in amplicon melting temperature (melt-MAMA) and size (agarose-MAMA). Our MAMA assays accurately genotyped strains both from culture and fish tissues at low cost, using either real-time (~AUD$1/per sample) or conventional (~AUD$0.50/per sample) PCR instrumentation. Our novel assays provide a rapid, reproducible, and cost-effective tool for routine genotyping of this pathogen, allowing faster identification and treatment of nocardiosis-effected permit fish within Vietnamese aquaculture/mariculture facilities, an essential step in mitigating N. seriolae-associated losses.

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Who’s who in the western Hermann’s tortoise conservation: a STR toolkit and reference database for wildlife forensic genetic analyses

10.1101/484030 ◽

2018 ◽

Author(s):

Biello Roberto ◽

Zampiglia Mauro ◽

Corti Claudia ◽

Deli Gianluca ◽

Biaggini Marta ◽

...

Keyword(s):

Dna Typing ◽

Geographic Origin ◽

Unknown Origin ◽

Reference Database ◽

Illegal Trade ◽

Wild Populations ◽

Long Distance ◽

Testudo Hermanni ◽

Forensic Genetic ◽

Area Of Origin

ABSTRACTIllegal trade is threatening tortoise populations worldwide since decades. Nowadays, however, DNA typing and forensic genetic approaches allow to investigate geographic origin of confiscated animals and to relocate them into the wild, provided that suitable molecular tools and reference data are available. Here we assess the suitability of a small panel of microsatellite markers to investigate patterns of illegal translocations and to assist forensic genetic applications in the endangered Mediterranean land tortoise Testudo hermanni hermanni. We used the microsatellite panel to (i) increase the understanding of the population genetic structure in wild populations with new data from previously unsampled geographic areas (overall 461 wild individuals from 28 sampling sites); (ii) detect the presence of non-native individuals in wild populations; and (iii) identify the most likely geographic area of origin of 458 confiscated individuals hosted in Italian seizure and recovery centers. Our analysis initially identified six major genetic clusters corresponding to different geographic macro-areas along the Mediterranean range. Long-distance migrants among wild populations, due to translocations, were found and removed from the reference database. Assignment tests allowed us to allocate approximately 70% of confiscated individuals of unknown origin to one of the six Mediterranean macro-areas. Most of the assigned tortoises belonged to the genetic cluster corresponding to the area where the respective captivity center was located. However, we also found evidence of long-distance origin of confiscated individuals, especially in centers along the Adriatic coast and facing the Balkan regions, a well-known source of illegally traded individuals. Our results clearly show the role for reintroduction projects of the microsatellite panel, which was useful to re-assign most of the confiscated individuals to the respective macro-area of origin. At the same time, the microsatellite panel can assist future forensic genetic applications to detect illegal trade and possess of Testudo hermanni individuals.

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A novel hybrid nanofibrous strategy to target progenitor cells for cost-effective in situ angiogenesis

Journal of Materials Chemistry B ◽

10.1039/c6tb02162j ◽

2016 ◽

Vol 4 (43) ◽

pp. 6967-6978 ◽

Cited By ~ 10

Author(s):

N. Sachot ◽

O. Castaño ◽

H. Oliveira ◽

J. Martí-Muñoz ◽

A. Roguska ◽

...

Keyword(s):

Calcium Phosphate ◽

Progenitor Cells ◽

Low Cost ◽

Cost Effective ◽

Cell Interaction ◽

High Yield ◽

Interface Cell

Ti-doped calcium phosphate ormoglasses combined with biodegradable PLA promote an efficient and low-cost angiogenesis by the generation of high Ca2+concentrated interfaces that induce a high yield of tubulogenesis, with the gain in interface–cell interaction and instructivity.

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