scholarly journals Recombination Pattern Characterization via Simulation Using Different Maize Populations

2020 ◽  
Vol 21 (6) ◽  
pp. 2222
Author(s):  
Wei Ren ◽  
Xiaoping Gong ◽  
Kun Li ◽  
Hongwei Zhang ◽  
Fanjun Chen ◽  
...  
Keyword(s):  
Recombination Rate ◽  
Cost Effective ◽  
Simulation Method ◽  
Construction Process ◽  
Effective Population ◽  
Recombination Rates ◽  
Crop Species ◽  
Different Types ◽  
Optimal Recombination ◽  
Almost All

Efficient recombination is critical to both plant breeding and gene cloning. However, almost all traditional recombination studies and genetic improvements require the slow and labor-intensive population construction process, and little is known about the recombination characteristics of populations of different types, generations, and origins. Here, we provide a simple and efficient simulation method for population construction based on doubled haploid (DH) and intermated B73 × Mo17 maize (IBM) populations to predict the recombination pattern. We found that the chromosomes had 0, 1, 2, and 3 recombination events that occurred at rates of 0.16, 0.30, 0.23, and 0.15, respectively, in the DH and the recombination rate of each chromosome in the IBM population ranged from 0 to 12.1 cM per 125 kb. Based on the observed recombination parameters, we estimated the number of recombination events and constructed the linkage maps of the simulated DH and recombination inbred line (RIL) populations. These simulated populations exhibited similar recombination patterns compared with the real populations, suggesting the feasibility of this simulation approach. We then compared the recombination rates of the simulated populations of different types (DH induced or self-crossed), generations, and origins (using the 8, 16, and 32 multiparent advanced generation intercross (MAGIC) populations), and suggested a rapid and cost-effective population construction procedure for breeders and geneticists, while maintaining an optimal recombination rate. This study offers a convenient method for optimizing the population construction process and has broader implications for other crop species, thereby facilitating future population studies and genetic improvement strategies.

scholarly journals The Theory and Applications of Measuring Broad-Range and Chromosome-Wide Recombination Rate from Allele Frequency Decay around a Selected Locus

2020 ◽  
Vol 37 (12) ◽  
pp. 3654-3671
Author(s):  
Kevin H -C Wei ◽  
Aditya Mantha ◽  
Doris Bachtrog
Keyword(s):  
Genetic Distance ◽  
Allele Frequency ◽  
Recombination Rate ◽  
High Throughput Sequencing ◽  
Genetic Material ◽  
Cost Effective ◽  
Genetic Distances ◽  
Recombination Rates ◽  
Marker Selection ◽  
Cost Effective Approach

Abstract Recombination is the exchange of genetic material between homologous chromosomes via physical crossovers. High-throughput sequencing approaches detect crossovers genome wide to produce recombination rate maps but are difficult to scale as they require large numbers of recombinants individually sequenced. We present a simple and scalable pooled-sequencing approach to experimentally infer near chromosome-wide recombination rates by taking advantage of non-Mendelian allele frequency generated from a fitness differential at a locus under selection. As more crossovers decouple the selected locus from distal loci, the distorted allele frequency attenuates distally toward Mendelian and can be used to estimate the genetic distance. Here, we use marker selection to generate distorted allele frequency and theoretically derive the mathematical relationships between allele frequency attenuation, genetic distance, and recombination rate in marker-selected pools. We implemented nonlinear curve-fitting methods that robustly estimate the allele frequency decay from batch sequencing of pooled individuals and derive chromosome-wide genetic distance and recombination rates. Empirically, we show that marker-selected pools closely recapitulate genetic distances inferred from scoring recombinants. Using this method, we generated novel recombination rate maps of three wild-derived strains of Drosophila melanogaster, which strongly correlate with previous measurements. Moreover, we show that this approach can be extended to estimate chromosome-wide crossover interference with reciprocal marker selection and discuss how it can be applied in the absence of visible markers. Altogether, we find that our method is a simple and cost-effective approach to generate chromosome-wide recombination rate maps requiring only one or two libraries.

scholarly journals Recombination Rate Variation and Infrequent Sex Influence Genetic Diversity in Chlamydomonas reinhardtii

2020 ◽  
Vol 12 (4) ◽  
pp. 370-380 ◽  
Author(s):  
Ahmed R Hasan ◽  
Rob W Ness
Keyword(s):  
Linkage Disequilibrium ◽  
Chlamydomonas Reinhardtii ◽  
Recombination Rate ◽  
Natural Populations ◽  
Effective Rate ◽  
Sexual Cycle ◽  
Rate Variation ◽  
Effective Population ◽  
Recombination Rates ◽  
Recombination Rate Variation

Abstract Recombination confers a major evolutionary advantage by breaking up linkage disequilibrium between harmful and beneficial mutations, thereby facilitating selection. However, in species that are only periodically sexual, such as many microbial eukaryotes, the realized rate of recombination is also affected by the frequency of sex, meaning that infrequent sex can increase the effects of selection at linked sites despite high recombination rates. Despite this, the rate of sex of most facultatively sexual species is unknown. Here, we use genomewide patterns of linkage disequilibrium to infer fine-scale recombination rate variation in the genome of the facultatively sexual green alga Chlamydomonas reinhardtii. We observe recombination rate variation of up to two orders of magnitude and find evidence of recombination hotspots across the genome. Recombination rate is highest flanking genes, consistent with trends observed in other nonmammalian organisms, though intergenic recombination rates vary by intergenic tract length. We also find a positive relationship between nucleotide diversity and physical recombination rate, suggesting a widespread influence of selection at linked sites in the genome. Finally, we use estimates of the effective rate of recombination to calculate the rate of sex that occurs in natural populations, estimating a sexual cycle roughly every 840 generations. We argue that the relatively infrequent rate of sex and large effective population size creates a population genetic environment that increases the influence of selection on linked sites across the genome.

FACTORS THAT AFFECT THE JOB BURNOUT AMONG ARCHITECTS AT DESIGN FIRMS

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
GULDEN GUMUSBURUN AYALP ◽  
Nur Bozhuyuk ◽  
Ilhami Ay
Keyword(s):  
Construction Industry ◽  
Turnover Intention ◽  
Construction Projects ◽  
Architectural Design ◽  
Fast Track ◽  
Cost Effective ◽  
Job Burnout ◽  
Construction Process ◽  
Design Firms ◽  
Almost All

Construction industry is characterized with its complicated, risky, hazardous and demanding nature. Construction projects are comprised of variety of activities that must be completed in a timely, cost-effective, and high-quality manner. Within fast track construction projects, architects who participate at almost all phases of construction process are often expected to work erratic and long hours. Therefore, these factors can frequently result in stressful work environment. Prolonged job stress cause job burnout could decrease individuals’ level of job satisfaction, productivity and increase turnover intention that consequentially lowers the organization’s performance. Emotional exhaustion, cynicism, and diminished professional efficacy were remarked to be valid in the most commonly accepted burnout model. This research aimed to investigate the factors that cause job burnout among architects working within architectural offices in Turkey. Identifying the most important burnout factors is another goal of this study. Therefore, to reach these aims a questionnaire was composed by researchers with literature review and applied to architects who are working at architectural design firms in Turkey. At the end of data collection 360 surveys are gathered. Obtained data were statistically analyzed. Consequently, six critical factors determined causing burnout among architects.

scholarly journals Background selection under evolving recombination rates

2021 ◽  
Author(s):  
Tom R Booker ◽  
Bret A Payseur ◽  
Anna Tigano
Keyword(s):  
Recombination Rate ◽  
Purifying Selection ◽  
Background Selection ◽  
Effective Population ◽  
Recombination Rates ◽  
Fitness Effects ◽  
Deleterious Alleles ◽  
Genome Wide ◽  
Modern House ◽  
Eukaryotic Genomes

Background selection (BGS), the effect that purifying selection exerts on sites linked to deleterious alleles, is expected to be ubiquitous across eukaryotic genomes. The effects of BGS reflect the interplay of the rates and fitness effects of deleterious mutations with recombination. A fundamental assumption of BGS models is that recombination rates are invariant over time. However, in some lineages recombination rates evolve rapidly, violating this central assumption. Here, we investigate how recombination rate evolution affects genetic variation under BGS. We show that recombination rate evolution modifies the effects of BGS in a manner similar to a localised change in the effective population size, potentially leading to an underestimation of the genome-wide effects of selection. Furthermore, we find evidence that recombination rate evolution in the ancestors of modern house mice may have impacted inferences of the genome-wide effects of selection in that species.

scholarly journals Interbreed variation in meiotic recombination rate and distribution in the domestic chicken <i>Gallus gallus</i>

2019 ◽  
Vol 62 (2) ◽  
pp. 403-411
Author(s):  
Lyubov P. Malinovskaya ◽  
Katerina V. Tishakova ◽  
Natalia A. Volkova ◽  
Anna A. Torgasheva ◽  
Yakov A. Tsepilov ◽  
...  
Keyword(s):  
Recombination Rate ◽  
European Part ◽  
Genetic Linkage Analysis ◽  
Recombination Rates ◽  
Homologous Chromosomes ◽  
Recombination Nodules ◽  
Individual Variations ◽  
European Part Of Russia ◽  
Chicken Breeds ◽  
Almost All

Abstract. The efficiency of natural and artificial selection is critically dependent on the recombination rate. However, interbreed and individual variation in recombination rate in poultry remains unknown. Conventional methods of analysis of recombination such as genetic linkage analysis, sperm genotyping and chiasma count at lampbrush chromosomes are expensive and time-consuming. In this study, we analyzed the number and distribution of recombination nodules in spermatocytes of the roosters of six chicken breeds using immunolocalization of key proteins involved in chromosome pairing and recombination. We revealed significant effects of breed (R2=0.17; p<0.001) and individual (R2=0.28; p<0.001) on variation in the number of recombination nodules. Both interbreed and individual variations in recombination rate were almost entirely determined by variation in recombination density on macrochromosomes, because almost all microchromosomes in each breed had one recombination nodule. Despite interbreed differences in the density of recombination nodules, the patterns of their distribution along homologous chromosomes were similar. The breeds examined in this study showed a correspondence between the age of the breed and its recombination rate. Those with high recombination rates (Pervomai, Russian White and Brahma) are relatively young breeds created by crossing several local breeds. The breeds displaying low recombination rate are ancient local breeds: Cochin (Indo-China), Brown Leghorn (Tuscany, Italy) and Russian Crested (the European part of Russia).

Types of refractive errors and methods for their diagnosis

2020 ◽  
pp. 30-36
Author(s):  
Olga Lemzyakova
Keyword(s):  
Optical System ◽  
Contact Lenses ◽  
Vision Impairment ◽  
Refractive Errors ◽  
Vision Correction ◽  
Light Rays ◽  
Different Types ◽  
Almost All ◽  
Degrees Of Severity ◽  
The Brain

Refraction of the eye means its ability to bend (refract) light in its own optical system. In a normal state, which is called emmetropia, light rays passing through the optical system of the eye focus on the retina, from where the impulse is transmitted to the visual cortex of the brain and is analyzed there. A person sees equally well both in the distance and near in this situation. However, very often, refractive errors develop as a result of various types of influences. Myopia, or short-sightedness, occurs when the light rays are focused in front of the retina as a result of passing through the optical system of the eye. In this case, a person will clearly distinguish close objects and have difficulties in seeing distant objects. On the opposite side is development of farsightedness (hypermetropia), in which the focusing of light rays occurs behind the retina — such a person sees distant objects clearly, but outlines of closer objects are out of focus. Near vision impairment in old age is a natural process called presbyopia, it develops due to the lens thickening. Both myopia and hypermetropia can have different degrees of severity. The variant, when different refractive errors are observed in different eyes, is called anisometropia. In the same case, if different types of refraction are observed in the same eye, it is astigmatism, and most often it is a congenital pathology. Almost all of the above mentioned refractive errors require correction with spectacles or use of contact lenses. Recently, people are increasingly resorting to the methods of surgical vision correction.

The CSF p-tau181/Aβ42 Ratio Offers a Good Accuracy “In Vivo” in the Differential Diagnosis of Alzheimer’s Dementia

2019 ◽  
Vol 16 (7) ◽  
pp. 587-595 ◽  
Author(s):  
Roberto Santangelo ◽  
Alessandro Dell'Edera ◽  
Arianna Sala ◽  
Giordano Cecchetti ◽  
Federico Masserini ◽  
...  
Keyword(s):  
Clinical Practice ◽  
Clinical Diagnosis ◽  
Fdg Pet ◽  
Amyloid Β ◽  
Cost Effective ◽  
Daily Clinical Practice ◽  
Different Types ◽  
Experimental Trials ◽  
Csf Findings

Background: The incoming disease-modifying therapies against Alzheimer’s disease (AD) require reliable diagnostic markers to correctly enroll patients all over the world. CSF AD biomarkers, namely amyloid-β 42 (Aβ42), total tau (t-tau), and tau phosphorylated at threonine 181 (p-tau181), showed good diagnostic accuracy in detecting AD pathology, but their real usefulness in daily clinical practice is still a matter of debate. Therefore, further validation in complex clinical settings, that is patients with different types of dementia, is needed to uphold their future worldwide adoption. Methods: We measured CSF AD biomarkers’ concentrations in a sample of 526 patients with a clinical diagnosis of dementia (277 with AD and 249 with Other Type of Dementia, OTD). Brain FDG-PET was also considered in a subsample of 54 patients with a mismatch between the clinical diagnosis and the CSF findings. Results: A p-tau181/Aβ42 ratio higher than 0.13 showed the best diagnostic performance in differentiating AD from OTD (86% accuracy index, 74% sensitivity, 81% specificity). In cases with a mismatch between clinical diagnosis and CSF findings, brain FDG-PET partially agreed with the p-tau181/Aβ42 ratio, thus determining an increase in CSF accuracy. Conclusions: The p-tau181/Aβ42 ratio alone might reliably detect AD pathology in heterogeneous samples of patients suffering from different types of dementia. It might constitute a simple, cost-effective and reproducible in vivo proxy of AD suitable to be adopted worldwide not only in daily clinical practice but also in future experimental trials, to avoid the enrolment of misdiagnosed AD patients.

Application of Natural Dye Obtained from Sweet Indrajao on Fabrics

2020 ◽  
Vol 6 (3) ◽  
pp. 180-191
Author(s):  
Kavitha Chandrasekaran
Keyword(s):  
Potassium Dichromate ◽  
Bacterial Pathogens ◽  
Ultrasonic Method ◽  
Ferrous Sulphate ◽  
Fine Powder ◽  
Cost Effective ◽  
Metal Salts ◽  
Cow Dung ◽  
Long Run ◽  
Almost All

Background:: In the long run, synthetic tints were found to be harmful to the chemicals. As a result natural tints have come to be used for their many intrinsic values. The main reason being, then availability of local plants as the main source of natural colorants. Their easy availability in the country being zero cost – effective and planted for other purposes are the main reasons for utilizing them as natural tints. Almost all the parts of the plants, namely stem, leaves, fruits, seeds, barks etc. are used for extracting natural colour. In addition, they are antimicrobial antifungal, insect – repellant deodorant, disinfectant having medicinal values. Methods:: Sweet Indrajao leaves were cleaned by washing with water and dried under direct sunlight and ground as fine powder. A fine strainer was used to remove the wastages. After all these processes, 1-kilogram leaves weighed 318 grams. Then, it is put in 75% ethanol 25% water and heated in a breaker which in kept over a water bath for 2 hours. After this, the contents were filtered and kept in a separate beaker. Bleached fleece draperies stained with stain extract were made to become wet and put into different stain baths which contain the required amount of stain extract and water. Acetic acid was added to it after 20 minutes. The fleece drapery was stained for about one hour at 60oC. The draperies thus stained were removed, squeezed, and put to treatment with metal salts without washing. Different metal salts were used for the treatment using 3% of any one of the chemical mordants like alum, stannous chloride, potassium dichromate, ferrous sulphate, nickel sulphate, copper sulphate and natural mordants such as myrobolan, turmeric, cow dung, Banana sap juice at 60oC for 30 minutes with MLR of 1:30. The stained draperies were washed repeatedly in all the three methods in water and dried in air. At last, the stained draperies were put to soap with soap solution at 60oC for 10 minutes. The draperies were repeatedly washed in water and dried under the sun. Results:: Sweet Indrajao leaves discharged colour easily in alcoholic water. The fleece draperies were stained with chemical and natural mordants. It was observed that the stain uptake was found to be good in post-mordanting method. Ultrasonication has clearly improved the stainability of the draperies at pH 3 and 3.5 values. The pH decreases the stain ability under both Conventional and Ultrasonic conditions. The colour strength increases with an increase in staining temperature in both cases of US and CH methods. Conclusion:: Sweet Indrajao.L has been found to have good ultrasonic potential as a stain plant. The stain uptake as well as the fastness properties of the fleece drapery were found to enhance when metal mordant was used in conjugation with ultra-sonication for the extract of Sweet Indrajao. It was also found that the enhancement of staining ability was better without mordant draperies. The dye extract showed good antibacterial activity against the three bacterial pathogens. Among the three bacterial pathogens, dye extract showed more effective against Escherichia coli pathogens and dye extract showed more effective against Aspergillus pathogens. Hence, the ultrasonic method of drapery staining may be appropriate and beneficial for society at large in future.

scholarly journals Chemical Variability of Peel and Leaf Essential Oils in the Citrus Subgenus Papeda (Swingle) and Few Relatives

Plants ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1117
Author(s):  
Clémentine Baccati ◽  
Marc Gibernau ◽  
Mathieu Paoli ◽  
Patrick Ollitrault ◽  
Félix Tomi ◽  
...  
Keyword(s):  
Essential Oils ◽  
13C Nmr ◽  
Chemical Diversity ◽  
Field Crop ◽  
High Chemical ◽  
Crop Species ◽  
Nmr Spectrometry ◽  
Chemical Variability ◽  
Almost All ◽  
Experimental Crosses

The Papeda Citrus subgenus includes several species belonging to two genetically distinct groups, containing mostly little-exploited wild forms of citrus. However, little is known about the potentially large and novel aromatic diversity contained in these wild citruses. In this study, we characterized and compared the essential oils obtained from peels and leaves from representatives of both Papeda groups, and three related hybrids. Using a combination of GC, GC-MS, and 13C-NMR spectrometry, we identified a total of 60 compounds in peel oils (PO), and 76 compounds in leaf oils (LO). Limonene was the major component in almost all citrus PO, except for C. micrantha and C. hystrix, where β-pinene dominated (around 35%). LO composition was more variable, with different major compounds among almost all samples, except for two citrus pairs: C. micrantha/C. hystrix and two accessions of C. ichangensis. In hybrid relatives, the profiles were largely consistent with their Citrus/Papeda parental lineage. This high chemical diversity, not only among the sections of the subgenus Papeda, but also between species and even at the intraspecific level, suggests that Papeda may be an important source of aroma diversity for future experimental crosses with field crop species.

scholarly journals Microsatellite Variation and Recombination Rate in the Human Genome

Genetics ◽  
2000 ◽  
Vol 156 (3) ◽  
pp. 1285-1298 ◽  
Author(s):  
Bret A Payseur ◽  
Michael W Nachman
Keyword(s):  
Recombination Rate ◽  
Microsatellite Polymorphism ◽  
Published Data ◽  
Strong Positive Correlation ◽  
Background Selection ◽  
Recombination Rates ◽  
Microsatellite Variation ◽  
Positive Correlation ◽  
Genome Recombination ◽  
Neutral Mutations

Abstract Background (purifying) selection on deleterious mutations is expected to remove linked neutral mutations from a population, resulting in a positive correlation between recombination rate and levels of neutral genetic variation, even for markers with high mutation rates. We tested this prediction of the background selection model by comparing recombination rate and levels of microsatellite polymorphism in humans. Published data for 28 unrelated Europeans were used to estimate microsatellite polymorphism (number of alleles, heterozygosity, and variance in allele size) for loci throughout the genome. Recombination rates were estimated from comparisons of genetic and physical maps. First, we analyzed 61 loci from chromosome 22, using the complete sequence of this chromosome to provide exact physical locations. These 61 microsatellites showed no correlation between levels of variation and recombination rate. We then used radiation-hybrid and cytogenetic maps to calculate recombination rates throughout the genome. Recombination rates varied by more than one order of magnitude, and most chromosomes showed significant suppression of recombination near the centromere. Genome-wide analyses provided no evidence for a strong positive correlation between recombination rate and polymorphism, although analyses of loci with at least 20 repeats suggested a weak positive correlation. Comparisons of microsatellites in lowest-recombination and highest-recombination regions also revealed no difference in levels of polymorphism. Together, these results indicate that background selection is not a major determinant of microsatellite variation in humans.

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