Tuesday, November 29, 2022

What Is Locus In Biology

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This Word Describes The Location Of A Gene In Your Dna

what is a locus | 12 | PRINCIPLES OF INHERITANCE AND VARIATION | BIOLOGY | PRADEEP | Doubtnu…

Long strands of DNA can contain many genes. We call a genes spot on a DNA molecule its locus.

Locus or loci

Chromosomes are pieces of coiled DNA. They contain many individual genes segments of DNA carrying instructions for making proteins. Together those genes help make a cell run. Locus is the word we use for the precise place where a gene is located on a chromosome. Figuring out the locus of a gene can be very important to understanding what it does.

In a sentence

A new germ-stopping compound binds to germ DNA at specific loci, so the bacteria cant breed.

Availability Of Data And Materials

The whole genome sequencing raw reads have been deposited in NCBIs sequence read archive under accession number PRJNA297202 . Background information, bud set genetic values , and environmental data at the site or origin for all clones used in the GWAS are available from Zendo under a CC BY-SA 4.0 license. All scripts used for the analysis described are available on GitHub under a MIT License .

Examples Of Locus In A Sentence

locuslocuslocus Los Angeles Timeslocus Vulturelocus CNNlocus Baltimore Sunlocus CNNlocus Washington Postlocus Los Angeles Timeslocus Forbes

These example sentences are selected automatically from various online news sources to reflect current usage of the word ‘locus.’ Views expressed in the examples do not represent the opinion of Merriam-Webster or its editors. Send us feedback.

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Field Experiment With Transgenic Ptft2 Lines

Construction of the PtFT RNAi lines are described in detail in . Briefly, the clone used for transformations is a hybrid aspen, P. tremula × tremuloides, clone T89, that sets bud at 15-h day lengths and this clone thus has a photoperiodic response that is comparable to SwAsp genotypes from southern Sweden . Transformed T89 plants were planted together with wild type T89 controls in a common garden at Våxtorp, Halland in 2014. Eighteen replicates of each line were planted in a complete randomized block design together with six WT controls per block. Starting in 2015, data were collected on growth cessation, bud formation, and bud set for all trees in the common garden. From early August, plants were visually inspected roughly every five days and top shoots were scored according to a pre-determined scoring sheet and classified as active growth , growth cessation , bud formation , and bud set . Scoring was continued until all plants had completely senesced in late October. Bud scoring data were converted to Julian date of bud set and analyzed using the following linear model:

where is an overall mean, i is the effect of treatment i , and j is the effect of block j and ij are individual residual errors.

Multiple Locus Linkage Analysis Of Genomewide Expression In Yeast

genetics
  • *To whom correspondence should be addressed. E-mail: , Email:

    Affiliation Department of Biostatistics, University of Washington, Seattle, Washington, United States of America

  • Affiliation Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America

  • Leonid Kruglyak

    *To whom correspondence should be addressed. E-mail: , Email:

    Affiliations Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America

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Locus Examples In Two Dimensional Geometry

We have already discussed the locus of the points which defines the path for a shape . Now let us see some more examples in 2-D geometry or plane geometry.

Perpendicular Bisector:

The set of points that bisects the line, formed by joining two points and are equidistant from two points, is called a perpendicular bisector.

Angle Bisector:

A locus or set of points that bisects an angle and are equidistant from two intersecting lines, which forms an angle, is called an angle bisector.

Ellipse:

Ellipse is defined as the set of points that satisfies the condition where the sum of the distances of two foci points is constant.

Parabola:

The set of points or loci, which are equidistant from a fixed point and a line, is called a parabola. The fixed point is the focus and the line is the directrix of the parabola.

Hyperbola:

A hyperbola has two focus points, which are equidistant from the centre of the semi-major axis. Hyperbola is defined as the set of points, which satisfies the condition where the absolute value of the difference between the distances to two given foci is a constant.

Locus Is What It Sounds Like

An axis of determination of a locus is all the points whose positions are determined by certain conditions. Several Independence movements have been led within a range of the Southwest. This definition of locus is used to determine the geographic center.

An equation or rule can be thought of as a locus, which is a set of points according to it.

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Solitary And Gregarious Phases

Solitariagregaria

One of the greatest differences between the solitary and gregarious phases is behavioural. The gregaria nymphs are attracted to each other, this being seen as early as the second instar. They soon form bands of many thousands of individuals. These groups behave like cohesive units and move across the landscape, mostly downhill, but making their way around barriers and merging with other bands. The attraction between the insects involves visual and olfactory cues. The bands seem to navigate using the sun. They pause to feed at intervals before continuing on, and may cover tens of kilometres over a few weeks.

Also, differences in morphology and development are seen. In the desert locust and the migratory locust, for example, the gregaria nymphs become darker with strongly contrasting yellow and black markings, they grow larger, and have a longer nymphal period the adults are larger with different body proportions, less sexual dimorphism, and higher metabolic rates they mature more rapidly and start reproducing earlier, but have lower levels of fecundity.

Dating The Selective Sweep In The North Populations

IB Biology 3.1 Genes .2 – Locus Position of Gene on Chromosome

To date the inferred selective sweep in the North populations, we used the ABC method described in Ormond et al. to jointly estimate s and T assuming a model of selection from a de novo mutation . We simulated 5×105 independent selective sweep events using the coalescent simulation program msms . For the coalescent simulations, the ancestries of samples were traced backwards in time using standard coalescent methods and allowing for recombination. Selection was modelled at a single site by applying forward simulations, assuming additive selection so that the fitness of heterozygous and homozygous genotypes carrying the selected allele were 1+s/2 and 1+s, respectively. We simulated a chromosome region consisting of L=25,000 sites and assumed a diploid effective population size of Ne=92,000, a mutation rate of =3.75×108 per base pair per generation , and a recombination rate of r=0.729×108 per base pair per generation. Together these parameters yielded a scaled population mutation rate equal to =4NeL=86.27 and a scaled population recombination rate =4NerL=19.76. For each simulation, values for both s and T were drawn from uniform prior distributions, log10~U and log10~U.

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Solved Example On Locus

Example:

Find the equation of a points locus so that the sum of its distances from and is 3. What exactly does the equation mean?

Solution

Suppose P be a point on the given locus.

It is given that

16y272y+81 = 362)

16y272y+81 = 36×2+36y272y+36

36×2+20y2 = 45

The above equation is written as follows

Hence, the above equation defines an ellipse.

Therefore, the equation of locus is,

36×2+20y2 = 45, which is an ellipse.

Circumference Of A Circle

A locus is a collection of points that form geometric shapes like lines, lines segments, circles, curves, etc., and have locations that satisfy the conditions for their location. The points can be viewed instead as places where a point can be located or moved instead of just as a set of points.

In terms of the locus of points or loci, the circle corresponds to all points that are equidistant from one fixed point, where the fixed point is the circle’s center and its radius is the set of points from the center. Let P denote the point at the center of the circle, and r the radius of the circle, that is, the distance from P to the set of all points or the locus of all points.

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Estimation Of Ancestral States For All Snps

Since the ancestral states of SNPs are usually used for selection detection, for each SNP, we classified alleles as either ancestral or derived on the basis of comparisons with two outgroup species: P. tremuloides and P. trichocarpa. We obtained publicly available short read Illumina data for one P. tremuloides and one P. trichocarpa individual from the NCBI Sequence Read Archive . We individually aligned the reads from these two samples to the de novo P. tremula assembly and used UnifiedGenotyper in GATK to call SNPs at all sites . For each SNP, two procedures were performed to define their ancestral states: because P. trichocarpa is more distantly related to P. tremula compared to P. tremuloides and from our previous study there were < 1% polymorphic sites shared between P. tremula and P. trichocarpa , we inferred the ancestral state as the P. trichocarpa allele at sites where the P. trichocarpa individual was homozygous and matched one of the P. tremula alleles otherwise, we inferred the ancestral state as the P. tremuloides allele at sites where the P. tremuloides individual was homozygous and matched one of the P. tremula alleles. If the above two requirements were not met, the ancestral state was defined as missing. In total, we obtained information of ancestral states for 96.3% of all SNPs.

Genetic Loci Involved In Archaeal Flagella Biosynthesis

Locus (genetics)

Archaeal genetic loci involved in flagella formation have so far been limited to genes located next to the flagellins. Typically, there are multiple flagellin genes followed by a number of flagella-associated genes . These genes are often transcribed as a single unit and deletion analysis has shown they are probably all essential for flagella formation, although the roles for most are unknown. FlaI is an ATPase homologous to ATPases in type IV pili loci and it has demonstrated ATPase activity, while FlaJ is homologous to a conserved membrane component also found in type IV pili systems. All flagellated Archaea contain flaHIJ as a unit and it has been suggested that these gene products form an assembly base for archaeal flagella, as suggested for the type IV pili system. In some Archaea, one of the flagellin genes is responsible for the hook. Hooks have not been detected in all archaeal flagella . All flagella-associated proteins, even ones lacking obvious transmembrane domains, localize to the cytoplasmic membrane, suggesting that some cytoplasmic components may be interacting with true membrane components to form a complex for assembly and/or anchoring. Interaction studies between the various Fla proteins have only begun as researchers attempt to sort out the roles of these unique proteins.

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Genome Sequencing Polymorphism Detection And Population Structure

In this study, we used a total of 94 unrelated P. tremula trees that were originally collected from 12 sites spanning c. 10° of latitude across Sweden . Earlier studies have shown that the SwAsp collection displays a strong latitudinal cline in the timing of bud set . We performed whole genome re-sequencing of all 94 aspens and obtained a total of 1139.2 Gb of sequence, with an average sequencing depth of ~30×per individual covering > 88% of the reference genome . After stringent variant calling and filtering, we identified a total of 4,425,109 high-quality single nucleotide polymorphisms with a minor allele frequency > 5%.

Fig. 1

Geographic distribution and genetic structure of 94 aspen individuals. a Location of the 12 original sample sites of the SwAsp collection and the location of the two common garden sites . The original collection sites span a latitudinal gradient of c. 10 latitude degrees across Sweden. b Genetic values for date of bud set for the 94 individuals included in the study across the two common gardens and three years . c Population structure in the SwAsp collection based on a PCA of 217,489 SNPs that were pruned to remove SNPs in high linkage disequilibrium . Although two axes are shown, only the first axis is significant

Screening For Snps Associated With Local Adaptation

We used three conceptually different approaches to test for genome-wide signatures of local adaptation. First, we detected candidate SNPs involved in local adaptation using the PCA as implemented in PCAdapt . PCAdapt examines the correlations between genetic variants and specific PCs without any prior definition of populations. As only the first PC was significant from the PCA , we only estimated the squared loadings 2j1 with PC1 to identify SNPs involved in local adaptation. Our results showed that most outlier SNPs that were highly correlated with the first population structure PC also had high FST values between populations . Assuming a chi-square distribution for the squared loadings 2j1, as suggested by , we used PCAdapt to compute P values for all SNPs and then calculated the FDR using the method of Storey and Tibshirani to generate a list of candidate SNPs showing significant associations to population structure. Only SNPs with FDR< 5% were retained as those significantly involved in local adaptation.

where \ and MAF is the effect size estimate and minor allele frequency for the SNP, N is sample size, and \ \) is standard error of effect size for the SNP.

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Sequence Quality Checking Read Mapping And Post

A total of 103 SwAsp individuals were successfully sequenced. Before read mapping, we used Trimmomatic v0.30 to identify reads with adapter contamination and to trim adapter sequences from reads. After checking the quality of the raw sequencing data using FastQC , the quality of sequencing reads was found to drop towards the ends of reads . We therefore used Trimmomatic v0.30 to trim bases from both ends of the reads if their qualities were < 20. Reads < 36 bases after trimming were discarded completely.

Locus Examples In Two

Genetics for beginners | Genes Alleles Loci on Chromosomes |

Here are some of the locus examples in two-dimensional geometry:

Perpendicular Bisector

The collection of points which bisect the line, molded by joining two points and equally distant from two points is called perpendicular bisector.

Angle Bisector

A locus of collection of points that bisect an angle and are equally distant from two intersecting lines, which forms an angle is known as an angle bisector.

Ellipse

The ellipse is defined as a collection of points that fulfill the condition where the sum of the distances of two focal points is fixed.

Parabola

It is the collection of points that are equally distant from a fixed point and a line is known as a parabola. The fixed point is represented as the locus and the line is represented as the directrix of the parabola.

Hyperbola

A hyperbola has two distinct focal points which are equally distant from the center of the semi-major axis. The collection of points fulfills the condition where the absolute value of the difference between the distances to two given foci is constant.

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Six Important Locus Theorems

There are six important locus theorems which are popular in geometry. These theorems may be confusing at first reading, but their concepts are actually easy to understand. Let us discuss the six important theorems in detail.

Locus Theorem 1:

The locus at the fixed distance d from the point p is considered to be a circle with p as its center and d as its diameter.

This theorem helps to determine the region formed by all the points which are located at the same distance from a single point

Locus Theorem 2:

The locus at a fixed distance d from the line m is considered as a pair of parallel lines that are located on either side of m at a distance d from the line m.

This theorem helps to find the region formed by all the points which are located at the same distance from a single line.

Locus Theorem 3:

The locus which is equidistant from the two given points say A and B, are considered as perpendicular bisectors of the line segment that joins the two points.

This theorem helps to determine the region formed by all the points which are located at the same distance from point A and as from point B. The region formed should be the perpendicular bisector of the line segment AB.

Locus Theorem 4:

The locus which is equidistant from the two parallel lines say m1 and m2, is considered to be a line parallel to both the lines m1 and m2 and it should be halfway between them.

Locus Theorem 5:

Locus Theorem 6:

Wise Search More Powerful Than 2d Search

One potential way to improve the exhaustive 2D scan is to use another method for selecting pairs of loci. In particular, one can select loci in a sequential manner, cutting down the number of models considered to 2 × 3,312, instead of more than 5 million. One readily available method for selecting loci in a sequential manner is forward stepwise regression. Here, one selects a primary locus that shows the most significant one-dimensional linkage, i.e., the one that has the largest LOD score. This is equivalent to identifying the locus that yields the smallest residual sum of squares when regressing the expression trait on the inheritance pattern at that locus . Next, a secondary locus is chosen that yields the largest LOD score conditional on the primary locus being linked. Again, this is equivalent to choosing a locus that minimizes the residual sum of squares when regressing the expression trait on both the secondary locus and the primary locus contained in the same model. A tertiary locus may be selected by including the previous two loci in the regression, and so on.

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