A low-cost open-source SNP genotyping platform for association mapping applications.
Ontology highlight
ABSTRACT:
SUBMITTER: Macdonald SJ
PROVIDER: S-EPMC1414086 | biostudies-literature | 2005
REPOSITORIES: biostudies-literature
Publications
A low-cost open-source SNP genotyping platform for association mapping applications.
Macdonald Stuart J SJ Pastinen Tomi T Genissel Anne A Cornforth Theodore W TW Long Anthony D AD
Genome biology 20051202 12
Association mapping aimed at identifying DNA polymorphisms that contribute to variation in complex traits entails genotyping a large number of single-nucleotide polymorphisms (SNPs) in a very large panel of individuals. Few technologies, however, provide inexpensive high-throughput genotyping. Here, we present an efficient approach developed specifically for genotyping large fixed panels of diploid individuals. The cost-effective, open-source nature of our methodology may make it particularly at ...[more]
Similar Datasets
Project description:BackgroundRemote monitoring of plants using hyperspectral imaging has become an important tool for the study of plant growth, development, and physiology. Many applications are oriented towards use in field environments to enable non-destructive analysis of crop responses due to factors such as drought, nutrient deficiency, and disease, e.g., using tram, drone, or airplane mounted instruments. The field setting introduces a wide range of uncontrolled environmental variables that make validation and interpretation of spectral responses challenging, and as such lab- and greenhouse-deployed systems for plant studies and phenotyping are of increasing interest. In this study, we have designed and developed an open-source, hyperspectral reflectance-based imaging system for lab-based plant experiments: the HyperScanner. The reliability and accuracy of HyperScanner were validated using drought and salt stress experiments with Arabidopsis thaliana.ResultsA robust, scalable, and reliable system was created. The system was built using open-sourced parts, and all custom parts, operational methods, and data have been made publicly available in order to maintain the open-source aim of HyperScanner. The gathered reflectance images showed changes in narrowband red and infrared reflectance spectra for each of the stress tests that was evident prior to other visual physiological responses and exhibited congruence with measurements using full-range contact spectrometers.ConclusionsHyperScanner offers the potential for reliable and inexpensive laboratory hyperspectral imaging systems. HyperScanner was able to quickly collect accurate reflectance curves on a variety of plant stress experiments. The resulting images showed spectral differences in plants shortly after application of a treatment but before visual manifestation. HyperScanner increases the capacity for spectroscopic and imaging-based analytical tools by providing more access to hyperspectral analyses in the laboratory setting.
| S-EPMC6348682 | biostudies-literature
Project description:Fish are the most species-rich vertebrate group, displaying vast ecological, anatomical and behavioural diversity, and therefore are of major interest for the study of behaviour and its evolution. However, with respect to other vertebrates, fish are relatively underrepresented in psychological and cognitive research. A greater availability of easily accessible, flexible, open-source experimental platforms that facilitate the automation of task control and data acquisition may help to reduce this bias and improve the scalability and refinement of behavioural experiments in a range of different fish species. Here we present GoFish, a fully automated platform for behavioural experiments in aquatic species. GoFish includes real-time video tracking of subjects, presentation of stimuli in a computer screen, an automatic feeder device, and closed-loop control of task contingencies and data acquisition. The design and software components of the platform are freely available, while the hardware is open-source and relatively inexpensive. The control software, Bonsai, is designed to facilitate rapid development of task workflows and is supported by a growing community of users. As an illustration and test of its use, we present the results of two experiments on discrimination learning, reversal, and choice in goldfish (Carassius auratus). GoFish facilitates the automation of high-throughput protocols and the acquisition of rich behavioural data. Our platform has the potential to become a widely used tool that facilitates complex behavioural experiments in aquatic species.
| S-EPMC10794453 | biostudies-literature
Project description:Water monitoring faces challenges that are driven by the infrastructure, protection, financial resources, science and innovation policies, among others. A modular, low-cost, fully open-source and small-sized Unmanned Surface Vessel (USV) called EMAC-USV (EMAC: Estación de Monitoreo Ambiental Costero), is proposed for monitoring bathymetry and water quality parameters (i.e. temperature, suspended solids concentration and hydrocarbon concentration) in complex water scenarios. A detailed description of each part of the platform as well as all electronic connections and functioning is presented.The field works were carried out in two small waste stabilization ponds and in a portion of the main tidal channel of the Bahía Blanca port. The EMAC-USV is the result of a cautious design, regarding the balancing performance, communications, payload capacity, among others.
| S-EPMC10749909 | biostudies-literature
Project description:Nasal airflow plays a critical role in olfactory processes, and both retronasal and orthonasal olfaction involve sensorimotor processes that facilitate the delivery of volatiles to the olfactory epithelium during odor sampling. Although methods are readily available for monitoring nasal airflow characteristics in laboratory and clinical settings, our understanding of odor sampling behavior would be enhanced by the development of inexpensive wearable technologies. Thus, we developed a method of monitoring nasal air pressure using a lightweight, open-source brain-computer interface (BCI) system and used the system to characterize patterns of retronasal airflow in human participants performing an oral fluid discrimination task. Participants exhibited relatively sustained low-rate retronasal airflow during sampling punctuated by higher-rate pulses often associated with deglutition. Although characteristics of post-deglutitive pulses did not differ across fluid conditions, the cumulative duration, probability, and estimated volume of retronasal airflow were greater during discrimination of perceptually similar solutions. These findings demonstrate the utility of a consumer-grade BCI system in assessing human olfactory behavior. They suggest further that sensorimotor processes regulate retronasal airflow to optimize the delivery of volatiles to the olfactory epithelium and that discrimination of perceptually similar oral fluids may be accomplished by varying the duration of optimal airflow rate.
| S-EPMC9505993 | biostudies-literature
Project description:Ultra-wideband (UWB) localization is one of the most promising approaches for indoor localization due to its accurate positioning capabilities, immunity against multipath fading, and excellent resilience against narrowband interference. However, UWB researchers are currently limited by the small amount of feasible open source hardware that is publicly available. We developed a new open source hardware platform, Wi-PoS, for precise UWB localization based on Decawave's DW1000 UWB transceiver with several unique features: support of both long-range sub-GHz and 2.4 GHz back-end communication between nodes, flexible interfacing with external UWB antennas, and an easy implementation of the MAC layer with the Time-Annotated Instruction Set Computer (TAISC) framework. Both hardware and software are open source and all parameters of the UWB ranging can be adjusted, calibrated, and analyzed. This paper explains the main specifications of the hardware platform, illustrates design decisions, and evaluates the performance of the board in terms of range, accuracy, and energy consumption. The accuracy of the ranging system was below 10 cm in an indoor lab environment at distances up to 5 m, and accuracy smaller than 5 cm was obtained at 50 and 75 m in an outdoor environment. A theoretical model was derived for predicting the path loss and the influence of the most important ground reflection. At the same time, the average energy consumption of the hardware was very low with only 81 mA for a tag node and 63 mA for the active anchor nodes, permitting the system to run for several days on a mobile battery pack and allowing easy and fast deployment on sites without an accessible power supply or backbone network. The UWB hardware platform demonstrated flexibility, easy installation, and low power consumption.
| S-EPMC6480456 | biostudies-other
Project description:Microencapsulation is a widely studied cell therapy and tissue bioengineering technique, since it is capable of creating an immune-privileged site, protecting encapsulated cells from the host immune system. Several polymers have been tested, but sodium alginate is in widespread use for cell encapsulation applications, due to its low toxicity and easy manipulation. Different cell encapsulation methods have been described in the literature using pressure differences or electrostatic changes with high cost commercial devices (about 30,000 US dollars). Herein, a low-cost device (about 100 US dollars) that can be created by commercial syringes or 3D printer devices has been developed. The capsules, whose diameter is around 500 µm and can decrease or increase according to the pressure applied to the system, is able to maintain cells viable and functional. The hydrogel porosity of the capsule indicates that the immune system is not capable of destroying host cells, demonstrating that new studies can be developed for cell therapy at low cost with microencapsulation production. This device may aid pre-clinical and clinical projects in low- and middle-income countries and is lined up with open source equipment devices.
| S-EPMC7696579 | biostudies-literature
Project description:Spectroradiometry is a vital tool in a wide range of biological, physical, astronomical and medical fields, yet its cost and accessibility are frequent barriers to use. Research into the effects of artificial light at night (ALAN) further compounds these difficulties with requirements for sensitivity to extremely low light levels across the ultraviolet to human-visible spectrum. Here, I present an open-source spectroradiometry (OSpRad) system that meets these design challenges. The system utilises an affordable miniature spectrometer chip (Hamamatsu C12880MA), combined with an automated shutter and cosine-corrector, microprocessor controller, and graphical user interface 'app' that can be used with smartphones or desktop computers. The system has high ultraviolet sensitivity and can measure spectral radiance at 0.001 cd m-2 and irradiance at 0.005 lx, covering the vast majority of real-world night-time light levels. The OSpRad system's low cost and high sensitivity make it well suited to a range of spectrometry and ALAN research.
| S-EPMC10357011 | biostudies-literature
Project description:The increasing transformation of biodiversity into a data-intensive science has seen numerous independent systems linked and aggregated into the current landscape of biodiversity informatics. This paper outlines how we can move forward with this programme, incorporating real time environmental monitoring into our methodology using low-power and low-cost computing platforms.
| S-EPMC4030251 | biostudies-literature
Project description:Spectrophotometry is a fundamental technique in many areas of science, with many applications and uses. The cost of spectrophotometers has acted as a barrier on the teaching and use of the technique. Here, we provide open-source plans to a 3D-printed cuvette holder with an interchangeable narrow-spectral bandwidth light-emitting diode (LED) block that can be used in conjunction with a smartphone's ambient light sensor (ALS) to perform spectrophotometry. A Lego version with an interchangeable LED block is also presented. Results from the smartphone spectrophotometer in comparison with commercially available spectrophotometers demonstrated functionality, and the model may have many applications, especially in indirect spectrophotometry, such as in the protein assay shown here. The plans for the 3D-printed model are freely available on GitHub, as are editable files to allow customisation by users. We would encourage users to share adaptations with the scientific community.
| S-EPMC6590830 | biostudies-literature
Project description:BackgroundCannabis sativa is seeing a global resurgence as a food, fiber and medicinal crop for industrial hemp and medicinal Cannabis industries respectively. However, a widespread moratorium on the use and research of C. sativa throughout most of the 20th century has seen the development of improved cultivars for specific end uses lag behind that of conventional crops. While C. sativa research and development has seen significant investments in the recent past, resulting in a suite of publicly available genomic resources and tools, a versatile and cost-effective mid-density genotyping platform for applied purposes in breeding and pre-breeding is lacking. Here we report on a first mid-density fixed-target SNP platform for C. sativa.ResultsThe High-throughput Amplicon-based SNP-platform for medicinal Cannabis and industrial Hemp (HASCH) was designed using a combination of filtering and Integer Linear Programming on publicly available whole-genome sequencing and RNA sequencing data, supplemented with in-house generated genotyping-by-sequencing (GBS) data. HASCH contains 1,504 genome-wide targets of high call rate (97% mean) and even distribution across the genome, designed to be highly informative (> 0.3 minor allele frequency) across both medicinal cannabis and industrial hemp gene pools. Average numbers of mismatch SNP between any two accessions were 251 for medicinal cannabis (N = 116) and 272 for industrial hemp (N = 87). Comparing HASCH data with corresponding GBS data on a collection of diverse C. sativa accessions demonstrated high concordance and resulted in comparable phylogenies and genetic distance matrices. Using HASCH on a segregating F2 population derived from a cross between a tetrahydrocannabinol (THC)-dominant and a cannabidiol (CBD)-dominant accession resulted in a genetic map consisting of 310 markers, comprising 10 linkage groups and a total size of 582.7 cM. Quantitative Trait Locus (QTL) mapping identified a major QTL for CBD content on chromosome 7, consistent with previous findings.ConclusionHASCH constitutes a versatile, easy to use and cost-effective genotyping solution for the rapidly growing Cannabis research community. It provides consistent genetic fingerprints of 1504 SNPs with wide applicability genetic resource management, quantitative genetics and breeding.
| S-EPMC11363669 | biostudies-literature