scholarly journals dCAPS method: advantages, troubles and solution

2008 ◽  
Vol 53 (No. 9) ◽  
pp. 417-420 ◽  
Author(s):  
M. Hrubá
Keyword(s):  
Genetic Mapping ◽  
Sex Chromosomes ◽  
Restriction Site ◽  
Cost Effective ◽  
Fundamental Principle ◽  
The Other ◽  
Model Organisms ◽  
Target Sequence ◽  
Evolutionary Studies ◽  
Sequence Polymorphisms

In our work, we focus on the evolutionary studies of sex chromosomes. As model organisms we use several species of the plant genus <i>Silene</i>. An important part of our research is represented by genetic mapping based on the assays of DNA length or sequence polymorphisms. Apart from the other methods we also use the dCAPS method, which is very useful for detection of the sequence polymorphisms (SNPs). This method is unique as it is able to detect SNPs that are not situated in any restriction site; a fundamental principle of this method is usage of primer designed with one or two mismatches that bring into the target sequence the mutation in vicinity of SNP. Using this method, we found out some improvements that can make analyses more cost-effective.

scholarly journals A GT-seq panel for walleye (Sander vitreus) provides a generalized workflow for efficient development and implementation of amplicon panels in non-model organisms

2020 ◽  
Author(s):  
Matthew L. Bootsma ◽  
Kristen M. Gruenthal ◽  
Garrett J. McKinney ◽  
Levi Simmons ◽  
Loren Miller ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
Cost Effective ◽  
Amplicon Sequencing ◽  
Parentage Analysis ◽  
Model Organisms ◽  
Sander Vitreus ◽  
Target Sequence ◽  
Genetic Stock ◽  
Genetic Stock Identification ◽  
Trade Offs

AbstractTargeted amplicon sequencing methods, such as genotyping-in-thousands by sequencing (GT-seq), facilitate rapid, accurate, and cost-effective analysis of hundreds of genetic loci in thousands of individuals, but studies describing detailed workflows of GTseq panel development are rare. Here, we develop a dual-purpose GT-seq panel for walleye (Sander vitreus) and discuss trade-offs associated with different development and genotyping approaches. Our GT-seq panel was developed using restriction site-associated DNA data from 954 individuals sampled from 23 populations in Minnesota and Wisconsin, USA. We then conducted simulations to test the utility of loci for parentage analysis and genetic stock identification and designed 600 primer pairs to maximize joint accuracy for these analyses. We conducted three rounds of primer optimization to remove loci that overamplified and our final panel consisted of 436 loci. Optimization focused on reducing variation in amplification rate among loci and minimizing the proportion of off-target sequence, both of which are important considerations for developing large GT-seq panels. We also explored different approaches for DNA extraction, multiplexed polymerase chain reaction (PCR) amplification, and cleanup steps during the GT-seq process and discovered the following: (1) inexpensive Chelex extractions performed well for genotyping, (2) the exonuclease I and shrimp alkaline phosphatase (ExoSAP) procedure included in some current protocols did not improve results substantially and was likely unnecessary, and (3) it was possible to PCR amplify panels separately and combine them prior to adapter ligation. Well-optimized GT-seq panels are valuable resources for conservation genetics and our findings should aid in their construction in myriad taxa.

2D Color-Intensity Representation of Ultrasonic Thickness Gauge Measurements

2020 ◽  
pp. 1192-1198
Author(s):  
M.S. Mohammad ◽  
Tibebe Tesfaye ◽  
Kim Ki-Seong
Keyword(s):  
Cost Effective ◽  
The Other ◽  
Thickness Gauge ◽  
Color Intensity ◽  
Digital Readout ◽  
Flat Surfaces ◽  
Video Cameras ◽  
Wide Range ◽  
Cost Effective Alternative ◽  
Ultrasonic Thickness

Ultrasonic thickness gauges are easy to operate and reliable, and can be used to measure a wide range of thicknesses and inspect all engineering materials. Supplementing the simple ultrasonic thickness gauges that present results in either a digital readout or as an A-scan with systems that enable correlating the measured values to their positions on the inspected surface to produce a two-dimensional (2D) thickness representation can extend their benefits and provide a cost-effective alternative to expensive advanced C-scan machines. In previous work, the authors introduced a system for the positioning and mapping of the values measured by the ultrasonic thickness gauges and flaw detectors (Tesfaye et al. 2019). The system is an alternative to the systems that use mechanical scanners, encoders, and sophisticated UT machines. It used a camera to record the probe’s movement and a projected laser grid obtained by a laser pattern generator to locate the probe on the inspected surface. In this paper, a novel system is proposed to be applied to flat surfaces, in addition to overcoming the other limitations posed due to the use of the laser projection. The proposed system uses two video cameras, one to monitor the probe’s movement on the inspected surface and the other to capture the corresponding digital readout of the thickness gauge. The acquired images of the probe’s position and thickness gauge readout are processed to plot the measured data in a 2D color-coded map. The system is meant to be simpler and more effective than the previous development.

scholarly journals Development of a Genoserotyping Method for Salmonella Infantis Detection on the Basis of Pangenome Analysis

2020 ◽  
Vol 9 (1) ◽  
pp. 67
Author(s):  
Seung-Min Yang ◽  
Jiwon Baek ◽  
Eiseul Kim ◽  
Hyeon-Be Kim ◽  
Seyoung Ko ◽  
...  
Keyword(s):  
Public Health ◽  
Polymerase Chain Reaction ◽  
Bacterial Species ◽  
Cost Effective ◽  
The Other ◽  
Gene Marker ◽  
Diagnostic Assay ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Substantial Economic Burden

In recent years, Salmonella Infantis has become a predominant serovariant in clinical and poultry isolates, thereby imposing a substantial economic burden on both public health and the livestock industry. With the aim of coping with the steep increase in serovar Infantis prevalence, a polymerase chain reaction (PCR)-based rapid and accurate diagnostic assay was developed in this study through pangenome profiling of 60 Salmonella serovars. A gene marker, SIN_02055, was identified, which is present in the S. Infantis genome but not in the pangenome of the other serovars. Primers specific to SIN_02055 were used to accurately detect serovar Infantis, and to successfully differentiate Infantis from the other 59 serovars in real-time PCR with a R2 of 0.999 and an efficiency of 95.76%. The developed method was applied to 54 Salmonella strains belonging to eight dominant serovars, and distinguished Infantis from the other seven serovars with an accuracy of 100%. The diagnostic primer set also did not show false positive amplification with 32 strains from eight non-Salmonella bacterial species. This cost-effective and rapid method can be considered an alternative to the classic serotyping using antisera.

scholarly journals Assessment of Live Candidate Vaccines for Paratuberculosis in Animal Models and Macrophages

2009 ◽  
Vol 78 (3) ◽  
pp. 1383-1389 ◽  
Author(s):  
Gabriella M. Scandurra ◽  
Geoffrey W. de Lisle ◽  
Sonia M. Cavaignac ◽  
May Young ◽  
R. Pamela Kawakami ◽  
...  
Keyword(s):  
Side Effects ◽  
Bacterial Load ◽  
Economic Effect ◽  
Cost Effective ◽  
The Other ◽  
Murine Models ◽  
Initial Screening ◽  
Vaccine Candidates ◽  
Allelic Exchange ◽  
Potential Vaccine

ABSTRACT Mycobacterium avium subsp. paratuberculosis (basonym M. paratuberculosis) is the causative agent of paratuberculosis, a chronic enteritis of ruminants. To control the considerable economic effect that paratuberculosis has on the livestock industry, a vaccine that induces protection with minimal side effects is required. We employed transposon mutagenesis and allelic exchange to develop three potential vaccine candidates, which were then tested for virulence with macrophages, mice, and goats. All three models identified the WAg906 mutant as being the most attenuated, but some differences in the levels of attenuation were evident among the models when testing the other strains. In a preliminary mouse vaccine experiment, limited protection was induced by WAg915, as evidenced by a reduced bacterial load in spleens and livers 12 weeks following intraperitoneal challenge with M. paratuberculosis K10. While we found macrophages and murine models to be rapid and cost-effective alternatives for the initial screening of M. paratuberculosis mutants for attenuation, it appears necessary to do the definitive assessment of attenuation with a ruminant model.

Ixazomib (IXA), carfilzomib (CAR), elotuzumab (ELO) or daratumumab (DAR) with lenalidomide and dexamethasone (LEN+DEX) versus LEN+DEX only in relapsed/refractory multiple myeloma (R/R MM): A comparative cost-effectiveness analysis.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 8043-8043
Author(s):  
Mavis Obeng-Kusi ◽  
Daniel Arku ◽  
Neda Alrawashdh ◽  
Briana Choi ◽  
Nimer S. Alkhatib ◽  
...  
Keyword(s):  
Cost Effectiveness ◽  
Cost Effective ◽  
Cost Utility ◽  
Cost Effectiveness Analysis ◽  
The Other ◽  
Sensitivity Analyses ◽  
Treatment Comparison ◽  
Comparative Cost ◽  
Effectiveness Analysis ◽  
Life Years

8043 Background: IXA, CAR, ELO and DARin combination with LEN+DEXhave been found superior in efficacy compared to LEN+DEX in the management of R/R MM. Applying indirect treatment comparisons from a network meta-analysis (NMA), this economic evaluation aimed to estimate the comparative cost-effectiveness and cost-utility of these four triplet regimens in terms of progression-free survival (PFS). Methods: In the absence of direct treatment comparison from a single clinical trial, NMA was used to indirectly estimate the comparative PFS benefit of each regimen. A 2-state Markov model simulating the health outcomes and costs was used to evaluate PFS life years (LY) and quality-adjusted life years (QALY) with the triplet regimens over LEN+DEX and expressed as the incremental cost-effectiveness (ICER) and cost-utility ratios (ICUR). Probability sensitivity analyses were conducted to assess the influence of parameter uncertainty on the model. Results: The NMA revealed that DAR+LEN+DEX was superior to the other triplet therapies, which did not differ statistically amongst them. As detailed in the Table, in our cost-effectiveness analysis, all 4 triplet regimens were associated with increased PFSLY and PFSQALY gained (g) over LEN+DEX at an additional cost. DAR+LEN+DEX emerged the most cost-effective with ICER and ICUR of $667,652/PFSLYg and $813,322/PFSQALYg, respectively. The highest probability of cost-effectiveness occurred at a willingness-to-pay threshold of $1,040,000/QALYg. Conclusions: Our economic analysis shows that all the triplet regimens were more expensive than LEN +DEX only but were also more effective with respect to PFSLY and PFSQALY gained. Relative to the other regimens, the daratumumab regimen was the most cost-effective.[Table: see text]

Sex-chromosome anaphase movements in crane-fly spermatocytes are coordinated: ultraviolet microbeam irradiation of one kinetochore of one sex chromosome blocks the movements of both sex chromosomes

1987 ◽  
Vol 88 (4) ◽  
pp. 441-452
Author(s):  
JULIA A. M. SWEDAK ◽  
ARTHUR FORER
Keyword(s):  
Sex Chromosomes ◽  
Sex Chromosome ◽  
The Other ◽  
Signal System ◽  
Spindle Fibre ◽  
Spindle Axis ◽  
Ultraviolet Microbeam ◽  
Block Motion ◽  
Block Movement ◽  
Spindle Fibres

Sex chromosomes in crane-fly spermatocytes move polewards at anaphase after the autosomes have reached the poles. In Nephrotoma abbreviate the sex chromosomes are 8 μm long by 3.5 μm wide and have two orientations when they move: the long axis of the sex chromosome is either perpendicular or parallel to the spindle axis. We assume (1) that when a sex chromosome is perpendicular to the spindle axis it has a chromosomal spindle fibre to each pole, one from each kinetochore, as in other species; and (2) that when a sex chromosome is parallel to the spindle axis each kinetochore has spindle fibres to both poles, i.e. that the latter sex chromosomes are maloriented. We irradiated one kinetochore of one sex chromosome using an ultraviolet microbeam. When both sex chromosomes were normally oriented, irradiation of a single kinetochore permanently blocked movement of both sex chromosomes. Irradiation of non-kinetochore chromosomal regions or of spindle fibres did not block movement, or blocked movement only temporarily. We argue that ultraviolet irradiation of one kinetochore blocks movement of both sex chromosomes because of effects on a ‘signal’ system. The results were different when one sex chromosome was maloriented. Irradiation of one kinetochore of a maloriented sex chromosome did not block motion of either sex chromosome. On the other hand, irradiation of one kinetochore of a normally oriented sex chromosome permanently blocked motion of both that sex chromosome and the maloriented sex chromosome. We argue that for the signal system to allow the sex chromosomes to move to the pole each sex chromosome must have one spindle fibre to each pole.

An International Campaign for Agricultural and Livestock Genomics (CALG)

2002 ◽  
Vol 06 (24) ◽  
pp. 958-965
Author(s):  
Jun Yu ◽  
Jian Wang ◽  
Huanming Yang
Keyword(s):  
Large Scale ◽  
Cost Effective ◽  
Model Organisms ◽  
Environmental Biology ◽  
Cdna Sequences ◽  
Governmental Agencies ◽  
Technology Innovations ◽  
A Genome ◽  
Starting Point ◽  
The Cost

A coordinated international effort to sequence agricultural and livestock genomes has come to its time. While human genome and genomes of many model organisms (related to human health and basic biological interests) have been sequenced or plugged in the sequencing pipelines, agronomically important crop and livestock genomes have not been given high enough priority. Although we are facing many challenges in policy-making, grant funding, regional task emphasis, research community consensus and technology innovations, many initiatives are being announced and formulated based on the cost-effective and large-scale sequencing procedure, known as whole genome shotgun (WGS) sequencing that produces draft sequences covering a genome from 95 percent to 99 percent. Identified genes from such draft sequences, coupled with other resources, such as molecular markers, large-insert clones and cDNA sequences, provide ample information and tools to further our knowledge in agricultural and environmental biology in the genome era that just comes to its accelerated period. If the campaign succeeds, molecular biologists, geneticists and field biologists from all countries, rich or poor, would be brought to the same starting point and expect another astronomical increase of basic genomic information, ready to convert effectively into knowledge that will ultimately change our lives and environment into a greater and better future. We call upon national and international governmental agencies and organizations as well as research foundations to support this unprecedented movement.

CHROMOSOMES AND DNA OF MICROTUS II. CONFIRMATION OF DELETION OF CONSTITUTIVE HETEROCHROMATIN IN M. AGRESTIS CELLS IN VITRO

1977 ◽  
Vol 19 (3) ◽  
pp. 537-541 ◽  
Author(s):  
J. E. K. Cooper
Keyword(s):  
Somatic Cell ◽  
Cell Line ◽  
Cell Lines ◽  
X Chromosome ◽  
Sex Chromosomes ◽  
Constitutive Heterochromatin ◽  
The Other ◽  
Microtus Agrestis ◽  
C Banding

The distribution of constitutive heterochromatin has been examined by C-banding in two somatic cell lines, grown in vitro, from a female Microtus agrestis. One line retains one intact X chromosome together with the short arm of the other X chromosome, while the other cell line retains only the short arm of one X chromosome. Thus, each cell line has lost substantial amounts of heterochromatin from the sex chromosomes, but this material has been deleted from the cells, and not translocated to other chromosomes. Nonetheless, both cell lines continue to propagate well in vitro.

scholarly journals The Divine-Human Unity in the Context of the Hasidic Doctrine of the Tsaddik’s Power

2020 ◽  
Vol 20 ◽  
pp. 100-124
Author(s):  
Igor Turov ◽  
Keyword(s):  
Interpersonal Communication ◽  
Water Drop ◽  
Fundamental Principle ◽  
The Other ◽  
Spiritual Practice ◽  
Community Members ◽  
Equal Footing ◽  
Concepts Of God ◽  
Basic Concepts ◽  
The One

For the founders of Hasidism, its fundamental principle is a spiritual practice that ensures an unceasing connection between the believer and his Creator. This doctrine is not purely theological: it serves as a rationale behind the societal hierarchy proposed by the Hasidim. The leader, having achieved the highest point of unity with the Lord, sets a pattern to be followed by the community members in their relationship with him as the one who rules over them, thus justifying the all-encompassing power of the Tsaddiks. The paper discusses three basic concepts of God-man unity. The essence of the first is the perception of the believer as immersing himself in the deity and dissolving there like a water drop in an ocean. The other two envision the unity as a peculiar interpersonal communication. The paper argues that within the Hasidic doctrine all three concepts are on an equal footing and shows the principles of their coexistence.

scholarly journals A review of Nadi Parikshan in various Ayurvedic Samhita with its clinical methods

2020 ◽  
Vol 4 (06) ◽  
Author(s):  
Pooja Babaso Kamble
Keyword(s):  
Diagnostic Tool ◽  
Common Factor ◽  
Research Work ◽  
Cost Effective ◽  
The Other ◽  
Diagnostic Tools ◽  
Healthy Individuals ◽  
Medical Field ◽  
Clinical Methods ◽  
Time Region

Nadi Pariksha is the most effective diagnostic tool known in the medical field. It is cost effective,  accurate,  safe,  and gives quick results. We can conduct Nadi Pariksha on healthy individuals as well as all patients irrespective of stage of the disease also,  and even pregnant woman,  children,  elderly can undergo without any harm or side effects. However,  this technique is not being widely practised at present,  because of lack of training,  practise and knowledge about it in the present day among Ayurveda vaidyas. An iconic factor for identification of a physician,  irrespective of the time,  Region,  Nadi Pariksha can be highlighted as a common factor or even System of Medicine or Civilization of the known world. Thus,  we can perceive that Nadi Pariksha or the pulse examination remains as an effective diagnostic tool since ages. Nadi Pariksha was not been discussed among the Brihatrayees of Ayurveda. Acharya Sharangdhara was the first to document in the doctrines of Ayurveda. Thus Acharya Sharangdhara is considered as ‘The Founder of Nadi Pariksha’in Ayurveda. Nadi Pariksha was titled under the Pancha-Nidana by Acharya Sharangdhara and Ashta Sthana Pariksha by Acharya Yogaratnakara. It was the Foremost among all the other diagnostic tools mentioned by him. Later Acharyas like Acharya Bhava Mishra,  Acharya Yogaratnakara,  Acharya Basavaraja,  Acharya Kanada Maharishi,  and Acharya Ravana have contributed in giving more descriptions and importance. In the recent days Dr. Vasant lad and Dr. Sarvadeva Upadhaya’s research work interest and scope of Nadi Pariksha.

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